Curriculum Vitae Goran Neshich

Last General Update: Jauary 14, 2009  

1. Personal Data2. Professional Qualifications3. Education History4. Professional Experience5. Membership To6. Language Competence7. Publications (Abstracts from Entrez)8. Work Presentend At Scientific Meetings9. Thesis Committee Participation10. Software Packages Published11. Seminars & Lectures given12. Courses13. Projects14. Professional References

1. PERSONAL DATA 1.1. Name: Goran Nesic Original name writing (Serbian): Goran Nešić U.S. documents anotation: Goran Neshich Portuguese pronunciation: Góran Neshitch (born in Beograd, Yugoslavia)

1.2. Professional: Embrapa Informática Agropecuária Caixa Postal: 6041 Av. Dr. André Tosello No: 209 Barão Geraldo, Cidade Universitária "Zeferino Vaz" CEP: 13083-886 Campinas (SP) - Brazil Telefone: 55-19-3211-5774 FAX: 55-19-3211-5754

E-mail: neshich@cnptia.embrapa.br Website: http://www.cbi.cnptia.embrapa.br/~neshich

2. PROFESSIONAL QUALIFICATIONS

Laboratory Management, Network Management, Software Design, Experiment Design,

Supervising and Teaching, Scientific Society Managment, Scientific Meeting Organization.

TECHNICAL AREAS AND SKILLS USED:

Computational Biology, BioInformatics, Structural Bioinformatics, Protein Engineering and Molecular Modeling;

Computational Biology & BioInformatics:

-In Silico Chemogenomics - Macromolecular Structure analysis, Macromolecular Surface analysis, Macromolecular Complexes and their Interfaces -Sequence analysis, Multiple Sequence Alignment, Structure Alignment -Phylogenetic trees and Evaluation of Multiple Sequence and Structure Alignments Based on Phylogenetic trees -Software Manufacturing for Sequence, Structure and Surface Analysis -Large Scale Automated Data-Base Consulting, Data Manipulation and Data Generation, Relational Database of protein descriptors

Protein:

-Purification (including isolation from the membranes) -Characterization -Sequence analysis (including DNA sequences), data-bases -Structure prediction and determination -Structural analysis -Molecular modeling, Homology modeling and Computer graphics -Molecular mechanics and molecular dynamics calculations -Protein design (Molecular Genetics, Site-directed mutagenesis) -Protein stability: kinetic and thermodynamic analysis -Modification and expression of proteins

Biochemistry:

-HPLC -SDS/PAGE -Ion-exchange chromatography -Peptide and protein sequencing

Biophysics, Bioenergetics and Photosynthesis:

-Experimental studies on electron transport in photosynthesis, Flash photolysis; Laser spectroscopy; Electronics; Quantum statistical mechanics -EPR (spin labeling; membrane fluidity) -Fluorescence (including quenching)

-electrochemical measurements -cryogenics

Protein-DNA interactions

-Simulation of Protein-DNA interactions (Molecular modeling; Sequence recognition)

Computer Networking, Data analysis, Statistics and Instrument interfacing:

-Networking (WAN and LAN), InterNet, TCP/IP, FTP -WWW/Gopher document editing, organization and distribution -UNIX, VMS and MS-DOS, MS-Windows and MS-Windows-NT operating systems -software design (using Fortran, Forth, Basic, C++, Pearl, JAVA, JavaScript) -molecular presentation software -GPIB and RS-232 interfacing to instruments

3. EDUCATION HISTORY

3.1. Post-graduation:                Post Doctorate: Biophisics - (1997-1998) University of Columbia                               Prof. Barry Honig - Dept. Biochemistry & Molecular Biophysics, New York, USA                              Subject: Development of algorithms to describe macromolecular interfaces.

3.1.1. Ph.D.:             Biophysics - University of Illinois at Urbana Champaign, Illinois, USA (1989)             Title of the thesis: "Biophysical Investigation of Electron Transfer between High Potential Hemes in C Subunit and Special Pair             of Reaction Center Protein of Photosynthetic Bacteria Rhodopseudomonas viridis".

    3.1.2. M.S.:                 Plant Bio-physics - Center for Multidisciplinary Studies, University of Belgrade, Yugoslavia (1981).                 Title of the thesis: "Influence of the Temperature on some Aspects of the Photosynthetic Process and Membranes in                  Maize (Zea mays L.)

3.2. B.S.:     3.2.1. Theoretical Physical-Chemistry Faculty of Life Science and Mathematics, University of Belgrade, Yugoslavia (1978)               Title of the thesis: "The Computation of the Energies and the Wave Functions for the Bending Vibrations of Three-atomic                 Molecules using Variation Method".

3.3. Other courses:

    3.3.1. United Nations Environment Programme (UNEP) course "Studies on Photosynthesis in Relation to Bioproductivity", chief

              coordinator Dr. David 0. Hall, King's College, University of London, U.K., conducted in the Laboratory of Biophysics, Maize              Research Institute, Belgrade, Yugoslavia, July.15 August.5.1981.

3.4. Professional Contacts:

3.4.1. European Molecular Biology Laboratory (EMBL), The EMBL data Library and Protein Design Group. Heidelberg - Germany. 3.4.2. RIKEN Life Science Center, The RIKEN Data Library, Tsukuba - city, Japan. 3.4.3. University of Illinois at Urbana-Champaign, Department of Biophysics and Beckman Institute. U.S.A. 3.4.4. National Center of Biotechnology Information (NCBI) Washington D.C., U.S.A. 3.4.5. International Center for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy 3.4.6. Broohaven National Laboratory, Protein Data Bank, Upton, New York, U.S.A. 3.4.7. Scripps Institute, San Diego, U.S.A. 3.4.8. University of Columbia, New York, New York, U.S.A. 3.4.9. Research Collaboratory for Structural Bioinformatics (RCSB) PDB, SDSC, UCSD, U.S.A. 3.4.10. CNB Madrid, Spain 3.4.11. Kyushu Institute of Technology, Japan 3.4.12. Scuola Normale Superiore, Pisa, Italy 3.4.13. H. Poincare University, Nancy, France 3.4.14. Zentrum für Bioinformatik, Universität Hamburg, Germany 3.4.15. Facultad de Ciencias Exactas, UNLP, Calles 49 y 115, 1900 La Plata, Argentina 3.4.16. Facultad de Ingeniería y Tecnologías, Universidad Católica del Uruguay, Montevideo, Uruguay 3.4.17. Center for Biological Sequence Analysis - DTU - Copenhagen - Denmark 3.4.18. Center for Multidisciplinary Studies, University of Belgrade, Serbia

4. PROFESSIONAL EXPERIENCE

  4.1. 1979-1985: Maize Research Institute, Zemun Polje, Belgrade, Yugoslavia.     4.1.1. Department of Physiology, Laboratory of Biophysics     4.1.2. Position: Research Associate     4.1.3. Project: "Computer Modeling of the Cell Membrane Response to Environmental Stress"

 

4.2. 1983-1989: University of Illinois at Urbana-Champaign, Illinois, U.S.A..     4.2.1. Department of Biophysics, Laboratory of Molecular Biophysics     4.2.2. Position: Research Assistant     4.2.3. Project: Bioenergetics of the photosynthetic processes.

 

4.3. 1988-1992: IICA/ (CENARGEN)/ EMBRAPA, Brasília, D.F., Brazil     4.3.1. Department of Molecular Biology, Laboratory for Protein Engineering and Biophysics     4.3.2. Position: International Consultant for EMBRAPA/CENARGEN through the Inter American Institute for Cooperation on Agriculture (IICA)     4.3.3. Project:          a) "Determination of the structure and the function of the storage protein 2S from Bertholletia excelsa H.B.K. with parallel introduction of tryptophan to satisfy                nutritional requirement in human diet”          b) "Molecular Genetics and Biophysical Studies on Reaction Center Protein from Rhodopseudomonas viridis".

 

4.4. 1993-1994: National Research Council (CNPQ) - National Computer Research Network (RNP) and CENARGEN/EMBRAPA Brasilia, DF, Brazil     4.4.1. Department of Molecular Biology, Laboratory for Protein Engineering and Bioinfomatics     4.4.2. Position: Group Leader and Chief Coordinator     4.4.3. Project:           a) Protein modeling           b) Establishment and coordination on the national level of the Brazilian Molecular Biology and Biotechnology Network (BMBBNet) and its principal node Brazilian Bioinformatics Resource Center (BBRC).

4.5. 1994 -1996 CENARGEN/EMBRAPA - Brasília, DF, Brazil     4.5.1. Department of Molecular Biology, Laboratory for Protein Engineering and Department of Bioinformatics     4.5.2. Position: Researcher/level III; Group Leader and Chief Coordinator     4.5.3. Project:           a) Protein modeling, DNA/Protein interaction studies           b) Coordination on the national level of the Brazilian Molecular Biology and Biotechnology Network (BMBBNet) and its principal node Brazilian Bioinformatics Resource Center (BBRC).

4.6. 1997-1998 : Columbia University, New York, U.S.A. -Barry Honig's Lab

4.7. 1998 -2000 CENARGEN/EMBRAPA - Brasília, DF, Brazil     4.7.1. Bioinformatics Laboratory     4.7.2. Position: Researcher/level III; Group Leader

4.8.- 2000 - Embrapa Informática Agropecuária -Campinas, SP, Brazil     4.8.1 Structural BioInformatics Center     4.8.2 Group Leader

5. MEMBERSHIP TO

5.1. Associação Brasileira da Bioinformatica e Biologia Computacional (AB3C) - Brazil. 5.2. Sociedade Brasileira da Bioquímica e Biologia Molecular (SBBq) - Brazil. 5.3. Biophysical Society, U.S.A.. 5.4. Biophysical Society, Yugoslavia. 5.5. Protein Society - International

5.6. International Society for Computational Biology (ISCB) - Member of the ISCB Board of Directors (2002-2005)

6. LANGUAGE COMPETENCE

6.1. Serbian, English, Russian and Portuguese (conversation, reading and writing competence). 6.2. Spanish and Italian (reading competence).

7. PUBLICATIONS

This Section Updated: JANUARY 14, 2009 

Web of Science:Total of 33 papersTotal of 198 citations H Factor H10(Neshich G OR Nesic G OR Neschich G) Date: January 07, 2009

7.1.Goran Neshich, Milan Schara, Marijeta Sentjurc, Zeljko Vucinic:"An EPR study of temperature dependent changes in fluidity of isolated maize thylakoid." Periodicum Biologorum, Vol.84, Nº2. 166-169, 1982, Zagreb, Yugoslavia. This article was cited: [ISI: 2]

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7.2.Zeljko Vucinic, Goran Neshich and Cedomir Radenovic: "Delayed fluorescence as an in situ probe of fluidity changes in maize photosynthetic membranes." Periodicum Biologorum, Vol. 84, Nº 2. 221-226, 1982, Zagreb, Yugoslavia. This article was cited: [ISI: 5] 

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7.3.I.C. Bezerra, L.A.B. de Castro, G. Neshich and D.C. Monte- Neshich: "A corm-specific gene encodes tarin, a major globulin of taro (Colacasia esculenta L. Schott)."Plant Molecular Biology, 28: 137-144, 1995.   This article was cited: [ISI: 14] [Google Scholar: 8] [Scopus:14]Journal ISI Impact Index for 2006: 3,577

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7.4.P.G.B. Carvalho, C. Bloch Jr., L. Morhy, Maria C.M. da Silva, Luciane V. de Mello, and Goran Neshich:"Amino Acid Sequence of the Phaseolus vulgaris Var. "Fogo na serra" Inhibitor and Interactive Surface Modeling for the enzyme-Inhibitor Complex."Journal of Protein Chemistry, Vol. 15, Nº 6, 1996 591-598.   This article was cited: [ISI: 1] [Google Scholar: 1] [Scopus:1]

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7.5.L.H. Marcellino, G. Neshich, M.F. Grossi de Sa, E. Krebbers and E. Gander:“Mutagenized 2S Albumins with improved tryptophan content are correctly expressed in trans-genic tobacco plants.” FEBS Letters 385 (1996) 154-158.   This article was cited: [ISI: 10] [Google Scholar: 12] [Scopus:12]Journal ISI Impact Index for 2006: 3,372 

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7.6.M. Vincentz, . Leite, L. Barros, D. Weinberg, E. de Almeida, M. Paes de Carvalho, F. Aragão, E. Gander and G. Neshich: “ACGT and Vicilin core sequences in a promoter domain required for seed specific expression of a 2S storage protein gene are recognized by the Opaque-2 regulatory protein."Plant Molecular Biology vol. 34, 1997 879-889.   This article was cited: [ISI: 11] [Google Scholar: 18] [Scopus:14]Journal ISI Impact Index for 2006: 3,577

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7.7.S.M. de Freitas, L.V. de Mello, M.C.M. da Silva, G. Vriend,G. Neshich and M.M. Ventura:“Analysis of the Black-eyed Pea Trypsin and Chymotrypsin Inhibitor-alpha-chymotrypsin com-plex." FEBS Letters 409 (1997) 121-127.   This article was cited: [ISI: 10] [Google Scholar: 19] [Scopus:22]Journal ISI Impact Index for 2006: 3,372 

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7.8.T.B. Cavalcante, A Rezende, R. Togawa, Patricia Rodrigues, Luciano Magalhaes and G. Neshich: "A new field-tested electronic system for data gathering, recording, transfer and dissemination via the World Wide Web." Taxon 47, May (1998), 381-386.   Journal ISI Impact Index for 2006: 2,519 

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7.9.G. Neshich, Roberto Togawa and Barry Honig: "Sequence To and withIN Graphics PDB Viewer (STING -PDB viewer)."PDB Quarterly NewsLetter, July 1998, page 6.     This article was cited: [Google Scholar: 6] 

 

7.10.G. Neshich, Roberto Togawa, Jaime Prilusky, Joel Suussman and Barry Honig: "Searching for the Right PDB File with the 3DB Browser and Displaying Structure and Sequence Data with STING." PDB Quarterly NewsLetter, July 1998, page 7.   

 

7.11.Da Silva M.C.M., Grossi de Sá M.F., Chrispeels M.J., Togawa R.C. and G. Neshich: "Analysis of Structural and Physico-chemical Parameters Involved in the Specificity of Binding be-tween Alpha-Amylases and their Inhibitors." Protein Engineering, Vol. 13, Nº 3, 167-177, March 2000.    This article was cited: [ISI: 12] [Google Scholar: 10] [Scopus:20]Journal ISI Impact Index for 2006: 2,718 

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7.12.Caldas, C.A., Coelho, V.P.C.V., Rigden, D., G. Neshich, Moro, A.M. and Brigido, M.:"Design and synthesis of germline-based hemi-humanized single chain Fv against the CD18 surface antigen." 

Protein Engineering Vol. 13, Nº5, 353-360, May 2000.   This article was cited: [ISI: 13] [Google Scholar: 16] [Scopus:11]Journal ISI Impact Index for 2006: 2,718 

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7.13.G. Neshich, Roberto Togawa, Adauto L. Mancini, Paula R. Kuser, Michel E. B. Yamagishi, Georgios Pappas Jr., Wellington V. Torres, Tharsis Fonseca e Campos, Leonardo L. Ferreira, Fabio M. Luna, Adil-ton G. Oliveira, Ronald T. Miura, Marcus K. Inoue, Luiz G. Horita, Dimas F. de Souza, Fabiana Do-miniquini, Alexandre Álvaro, Cleber S. Lima, Fabio O. Ogawa, Gabriel B. Gomes, Juliana C. F. Palan-drani, Gabriela F. dos Santos, Esther M. de Freitas, Amanda R. Mattiuz, Ivan C. Costa, Celso L. de Almeida, Savio Souza, Christian Baudet and Roberto H. Higa: "STING Millennium: a Web based suite of programs for comprehensive and simultaneous analysis of protein structure and sequence." Nucleic Acids Research Vol. 31, Nº 13, page 3386 - 3392, 2003.   This article was cited: [ISI: 28] [Google Scholar: 39] [Scopus: 27]Journal ISI Impact Index for 2006: 6,317 

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7.14.Fernandez J. H., Hayashi M.A.F., Camargo A.C.M. 1 and G. Neshich:"Structural basis of the lisinopril binding specificity in N and C domains of human somatic ACE." BBRC: Biochemical and Biophysical Research Communications 308 (2003)219-226.   This article was cited: [ISI: 7] [Google Scholar: 8] [Scopus: 8]Journal ISI Impact Index for 2006: 2,855 

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7.15.Paula Kuser Falcão, Michel Yamagishi, Roberto Higa e Goran Neshich:"Sting Millennium Suite: ferramentas para análise estrutural de proteínas." Com Ciência, August, 2003.     

 

7.16.R. C. Togawa, P. R. Kuser, R. H. Higa, M. E. B. Yamagishi, A. L. Mancini, and G. Neshich*:"STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes." BMC Bioinformatics. 2004 Aug 09;5(1):107.     This article was cited: [ISI: 12] [Google Scholar: 10] [Scopus:8]Journal ISI Impact Index for 2006: 3,617 

BMC-BI total downloads: 2685 (August 09, 2004 to January 14, 2009) 

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7.17.R.H. Higa, A.G. Oliveira1, L.G. Horita1, R.T. Miura1, M.K. Inoue1 P.R. Kuser, A.L. Mancini, M.E.B. Yamagishi, R. Togawa1, and G. Neshich*: "Defining 3D residue environment in protein structures using SCORPION and FORMIGA." Bioinformatics. 2004 Aug 12;20(12):1989-1991. Epub 2004 Mar 25.     This article was cited: [ISI: 2] [Google Scholar: 2] [Scopus: 2]Journal ISI Impact Index for 2006: 4,894 

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7.18.R. H. Higa, R. C. Togawa2, P. R. Kuser, M. E. B. Yamagishi, A. L. Mancini, G. Pappas Jr.3, R. T. Miura2, L. G. Horita2, andG. Neshich*: "ConSSeq: a web-based application for analysis of amino acid conservation based on HSSP database and within context of structure."Bioinformatics. 2004 Aug 12;20(12):1983-5. Epub 2004 Mar 25.     This article was cited: [ISI: 4] [Google Scholar: 6][Scopus: 4]Journal ISI Impact Index for 2006: 4,894 

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7.19.R. C. Togawa2, P. R. Kuser, R. H. Higa, M. E. B. Yamagishi, A. L. Mancini, and G. Neshich*:"STING Contacts: a web-based application for identification and analysis of amino acid contacts within protein structure and across protein interfaces." Bioinformatics. 2004 Sep 1;20(13):2145-7. Epub 2004 Apr 08.     This article was cited: [ISI: 8] [Google Scholar: 10] [Scopus: 8]Journal ISI Impact Index for 2006: 4,894 

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7.20.Goran Neshich, Walter Rocchia, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Christian Baudet, Ivan P. Pinto, Arnaldo J. Montagner, Juliana F. Palandrani, Joao N. Krauchenco, Renato C. Torres, Savio Souza, Roberto C. Togawa and Roberto H. Higa: "JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of pro-tein structure." Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W595-601.     This article was cited: [ISI: 13] [Google Scholar: 16][Scopus: 15]

Journal ISI Impact Index for 2006: 6,317 

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7.21.Marcellino LH, Neshich G, Neto AF, Gander ES.: "An opaque-2-like transcription factor from pearl millet." Protein Pept Lett. 2004 Aug;11(4):345-52.     Journal ISI Impact Index for 2006: 1,130 

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7.22.SILVA, Maria Cristina Mattar da; MELLO, Luciane V de; COUTINHO, Marise Ventura; RIGDEN, Daniel John; Goran Neshich; CHRISPEELS, Maarten John; GROSSI DE SA, Maria Fatima: "Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding speci-ficity to alpha-amylases." Pesquisa Agropecuária Brasileira, Brazil, v. 39, n. 3, p. 201-208, 2004.     This article was cited: [ISI: 1] [Google Scholar: 2] [Scopus:2]Journal ISI Impact Index for 2006: 0,286 

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7.23.Goran Neshich, Adauto L. Mancini, Michel E. B. Yamagishi, Paula R. Kuser, Renato Fileto, Ivan P. Pinto, Juliana F. Palandrani, João N. Krauchenco, Christian Baudet, Arnaldo J. Montagner and Roberto H. Higa: " STING Report: convenient web-based application for graphic and tabular presentations of pro-tein sequence, structure and function descriptors from the STING database." Nucleic Acids Res. 2005 Jan 1;33 (Database Issue):D269-74.     This article was cited: [ISI: 9] [Google Scholar: 14] [Scopus: 9]Journal ISI Impact Index for 2006: 6,317 

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7.24.NESHICH, Goran; BORRO, Luiz C; HIGA, Roberto; KUSER, Paula; YAMAGISHI, Michel; FRANCO, Eduardo H; KRAUCHENCO, Joao; FILETO, Renato; RIBEIRO, Andre; BEZERRA, George; VEL-LUDO, Thiago; JIMENEZ, Tomas; FURUKAWA, Noburo; TESHIMA, Hirofumi; KITAJIMA, Koji; BAVA, Abdulla; SARAI, Akinori; TOGAWA, Roberto; MANCINI, Adauto:" Diamond STING Server."Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W29-35.     This article was cited: [ISI: 10] [Google Scholar: 21] [Scopus: 10]

Journal ISI Impact Index for 2006: 6,317 

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7.25.HERNANDEZ, Jorge Fernandez; NESHICH, Goran; ACM, Camargo:"USING BRADYKININ POTENTIATING PEPTIDE (BPP) STRUCTURES TO DEVELOP NEW ANTIHIPERTEN-SIVE DRUGS." 

Genet. Mol. Res, Riberao Preto, v. 3, n. 4, p. 554-563, 2005.     This article was cited: [Google Scholar: 6] [Scopus:9]This article was cited: [Google Scholar: 6] 

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7.26.Yamagishi ME, Martins NF, Neshich G, Cai W, Shao X, Beautrait A, Maigret B.:"A fast surface matching procedure for protein-ligand docking." J Mol Model (Online). 2006 May 4.     This article was cited: [ISI: 2] [Google Scholar: 2] [Scopus: 2]Journal ISI Impact Index for 2006: 1,384

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7.27.HIGA, Roberto; KUSER, Paula; MICHEL, Yamagishi; MANCINI, Adauto; NESHICH, Goran: " Building Multiple Sequence Alignments with a flavour of HSSP alignments."Genet. Mol. Res. 5 (1), p: 127-137, 2006.     This article was cited:[ISI: 2] [Google Scholar: 2] [Scopus:2]

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7.28.Luiz C. Borro, Stanley R.M. Oliveira, Michel E.B. Yamagishi, Adaulto L. Mancini, José G. Jardine, Ivan Mazoni, Edgard H. dos Santos, Roberto H. Higa, Paula R. Kuser and Goran Neshich: "Predicting enzyme class from protein structure using Bayesian classification."Genet. Mol. Res. 5 (1), p:193-202, 2006.     This article was cited:[ISI: 6] [Google Scholar: 6] [Scopus:4]

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7.29.Renato Fileto, Paula R. Kuser, Michel E. B. Yamagishi, André A. Ribeiro, Thiago G. Quinalia, Eduardo H. Franco, Adauto L. Mancini, Roberto H. Higa, Stanley R. M. Oliveira, Edgard H. Santos, Fabio D. Vieira, Ivan Mazoni, Sergio A. B. Cruz, Goran Neshich:"PDB-metrics: a web tool for exploring the PDB contents."

Genet. Mol. Res. 5 (2), p:333-341, 2006.     

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7.30.Goran Neshich, Ivan Mazoni, Stanley R. M. Oliveira, Michel E. B. Yamagishi, Paula R. Kuser-Falcão, Luiz C. Borro, Douglas U. Morita, Kassyus R. R. Souza, Gustavo V. Almeida, Diego N. Rodrigues, José G. Jardine, Roberto C. Togawa, Adauto L. Mancini, Roberto H. Higa, Sérgio A. B. Cruz, Fábio D. Vieira, Edgard H. dos Santos, Raquel C. de Melo and Marcelo M. Santoro:"The Star STING server: A multiplatform environment for protein structure analysis."Genet. Mol. Res. 5 (4), 717-722, 2006.     This article was cited:[ISI: 6] [ Google Scholar: 10] [Scopus: 7]

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7.31.NESHICH, G, Bourne PE, Brunak, S.:" ISMB 2006."PLoS Comput Biol. Feb;2(2), 2006.   Journal ISI Impact Index for 2006: 4,914 

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7.32.M.C. Simões; D. Bahia; A.Z. Neto; K. Torres; F. Artiguenave; G. Neshich; P.R. Kuser, G.C. Oliveira:"Single nucleotide polymorphisms identification in expressed genes of Schistosoma mansoni."Molecular and Biochemical Parasitology, 154 134-140, 2007.     This article was cited: [Google Scholar: 1] [Scopus:2] Journal ISI Impact Index for 2006: 2,641 

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7.33.Jorge H. Fernandez, Marcia O. Mello, Leticia Galgaro, Aparecida S. Tanaka, Marcio C. Silva-Filho, Goran Neshich:"PROTEINASE INHIBITION USING SMALL BOWMAN-BIRK TYPE STRUCTURES."Genet. Mol. Res. 6 (4): 846-858 (2007)     This article was cited: [Scopus:1] 

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7.34.R.C. Melo, C. Ribeiro, C.S. Murray, C.J.M. Veloso, C.H.. da Silveira, Goran Neshich, W. Meira Jr, R.L. Carceroni and M.M. Santoro:"Finding protein-protein interactions by contact-maps matching."

Genet. Mol. Res. 6 (4): 946-963 (2007)     This article was cited: [Google Scholar: 1] [Scopus:1] 

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7.35.Walter Rocchia and Goran Neshich:"Electrostatic Potential Calculation for biomolecules - creating a database of pre-calculated values reported on a per residue basis for all PDB protein structures."Genet. Mol. Res. 6 (4): 923-936 (2007)     

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7.36 .Stanley R. M. Oliveira, Gustavo V. Almeida, Kassyus R. R. Souza, Diego N. Rodrigues, Paula R. Kuser-Falcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José G. Jardine and Goran Neshich:"STING_RDB: A relational database of structural parameters for protein analysis with support for Data Warehousing and Data Mining."Genet. Mol. Res. 6 (4): 911-922 (2007)     

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7.37.NESHICH, G:"Computational Biology in Brazil."PLoS Comput Biol. Oct; v3 (issue 10, e185), 2007.     This article was cited: [ISI: 1] [Google Scholar:1] [Scopus: 1]Journal ISI Impact Index for 2006: 4,914 

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7.38.MOUTRAN, Alexandre; BALAN, Andrea; PEREZ, Carolina Santacruz; FERREIRA, Rita Café;RAMOS, Carlos; FERREIRA, Luís Carlos Souza; NESHICH, Goran: "Crystallographic structure and substrate-binding interactions of the 3 molybdate-binding    pro-tein of the phytopathogen 4 Xanthomonas axonopodis pv. citri.”Biochim Biophys Acta. 2008 Feb;1784(2):393-9.    

Listed in:   and   , 

7.39.R. C. Togawa, C. Ribeiro, I. Mazoni, T. Pelligrinelli, and NESHICH, Goran: " The Table of Interface Forming Residues as the Specificity Indicator for Serine Proteases Bound to Different Inhibitors "

Accepted: BIOCOMP 08, 2008. Listed in:

7.40.Carlos H. da Silveira, Douglas E. V. Pires , Raquel C. Melo , Cristina Ribeiro , Caio J. M. Veloso , Julio C. D. Lopes , Wagner Meira Jr , Goran Neshich , Carlos H. I. Ramos , Raul Habesch, Marcelo M. San-toro: " Protein cutoff scanning: A comparative analysis of cutoff dependent and cutoff free methods for prospecting contacts in proteins. "PROTEINS: Structure, Function, and Bioinformatics,2008 Aug 14;74(3):727-743. 2008   

 

Listed in: 

 

7.41.Janaina Gomide ; Raquel Melo Minardi ; Marcos Augusto dos Santos ; Wagner Meira Jr. ; Julio Cesar Dias Lopes ; SANTORO, Marcelo ; NESHICH, Goran:" Using Linear Algebra for Protein Structural Comparison and Classification."Accepted: Genet. Mol. Res., 2009.Journal ISI Impact Index for 2006: 3,617

7.42.Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos, Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran:" BlueStar STING environment for protein structure analysis: expanded fetures and compatibility with remediated PDB format"Submitted: BMC Bioinformatics, 2009.Journal ISI Impact Index for 2006: 3,617

7.43.Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos, Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran: " The signals for initiation of secondary structure element nucleation in protein structures"To be submitted: Plos Computational Biology, in progress, 2009Journal ISI Impact Index for 2006: 4,914.

7.44.Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos, Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran:" Java Secondary Structure Dossier: environment for analysis of protein secondary structure"To be submitted: Bioinformatics, in progress, 2009.Journal ISI Impact Index for 2006: 4,894

7.45.Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos, Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran:" Chameleon sequences: secondary structure fidelity to a primary amino-acid sequence"

To be submitted: Journal of Molecular Biology, in progress, 2009.Journal ISI Impact Index for 2006: 4,890

7.46.Luiz Cesar Borro, Ivan Mazoni, Jose G. Jardine, Edgard H. Santos, Daniel de Alvarenga Campos, Mauri Carvalho, Thais Vital Pelligrinelli; NESHICH, Goran: " STING_RDB: the database containing 730 parameters describing protein structure, function, se-quence and stability"To be submitted: Nucleic Acid Research - Database issue, in progress, 2009.Journal ISI Impact Index for 2006: 6,317

8. WORK PRESENTED AT SCIENTIFIC MEETINGS

8.1. Z. Vucinic, G. Neshich, C. Radenovic: "Influence of temperature at photosynthetic process: Photo-induced bioluminescence as an in situ method to monitor changes of the thylakoid membranes". XI Yugoslav Biophysics Symposium, pp 101, Donji Milanovac,  11-14 October,1981, Yugoslavia.

8.2. G. Neshich, M. Schara, M. Sentjurc, Z. Vucinic: "Studies on conformational changes in thylakoid membranes of the chloroplasts from different maize genotypes using EPR spectroscopy". XI Yugoslav Biophysics Symposium, pp 102, Donji Milanovac, 11-14 October, 1981, Yugoslavia.

8.3. Z. Vucinic, G. Neshich, C. Radenovic: "Photoinduced bioluminescence as in situ method for monitoring state of fluidity in thylakoid  membranes". - Book of abstracts, problems in biophysics, SEP meeting, 1982, pp. III-33, Puschino, USSR.

8.4. Z. Vucinic, G.Neshich: "Possible application of the fluorescence methods for photosynthesis research in maize breeding program". - Second seminar of Yugoslav Society for plant physiology, Serbian Academy of Science, SANU, in Belgrade,March 27-29. 1983,  Yugoslavia.

8.5. Z. Vucinic, G. Neshich, J. Svetek, M. Schara: "Proline effects on maize thylakoid membrane fluidity and water structure ordering". - Book of abstracts of XII Yugoslav biophysics symposium, p. 51, Sept. 29 - Oct. 01. 1983. Opatija, Yugoslavia.

8.6. G. Neshich, D. DeVault and C. Wraight: "Kinetics of Electron Transfer from high potential Cytochrome c hemes to P+ functionally associated to photochemical reaction center in Rhodopseudomonas viridis" - Biophysical Society meeting, Cincinnati, OH, USA, February.05- 12. 1989.

8.7. F.X.S. Scares, M.C.M. da Silva, T.L. Rocha, L.H. Marcellino, N.S. Paes, I. Caracelli, M. Carneiro, E. Gander, M-J.A.M. Sampaio, L-A.B. De Castro and G. Neshich:   "Theoretical model of the secondary and tertiary structure of Brazil nut 2s storage albumins" in Abstracts of the First International Symposium on Crystallography and Molecular Biology, November 1990, Guaruja, SP, Brazil.

8.8. L.H.Marcellino, M.C.M. da Silva, T.L. Rocha, N.S. Paes, M. Carneiro, E. Gander, M-J.A.M. Sampaio, L-A.B. De Castro and G. Neshich: "Introduction of tryptophan in the brazil nut 2s storage albumins by site- directed mutagenesis" in Abstracts of the First International Symposium on Crystallography and Molecular Biology, November 1990, Guaruja, SP, Brazil.

8.9. M.C.M. da Silva, T.L. Rocha, L.H. Marcellino, N.S. Paes, I. Caracelli, M. Carneiro, E. Gander, M-J.A.M. Sampaio, LA.B. De Castro and G. Neshich:       "Brazil nut 2s storage albumin isoform purification and circular dichroism assisted secondary structure confirmation" in Abstracts of the First International Symposium on Crystallography and Molecular Biology, November 1990, Guaruja, SP, Brazil.

8.10. M.C.M. da Silva, L.V. de Mello, C. Bloch Jr., L. Morhy and G. Neshich: "Disulphide bridges determination in a 2S albumin storage protein from Brazil       nut (Bertholetia excelsa H.B.K.) Preliminary studies". In "Resumos da XXI Reunião Anual da Sociedade Brasileira de bioquímica e biologia molecular” Caxambu, MG,  Brazil 16-19 May, 1992.

8.11. I.C. Bezerra, L.A.B. De Castro, G. Neshich, E.R. Almeida and D.C. Monte-Neshich: "Structure of the gene coding for a major protein from taro tuber (Colocasia esculents)". In "Programa e Resumos da XXII Reunião Anual da Sociedade Brasileira de bioquímica e biologia molecular" Caxambu, MG, Brazil 1-4 May, 1993.

8.12. P.G.B. Carvalho, C. Bloch Jr. and L. Morhy in collaboration with G. Neshich: "The complete amino-acid sequence of a Bowman-Birk inhibitor from seeds of Phaseolus vulgaris Var. "Fogo na serra"." In "Programa e Resumos da XXII Reunião Anual da Sociedade Brasileira de bioquímica e biologia molecular" Caxambu, MG, Brazil 1-4 May, 1993.

8.13. M.C.M. da Silva, L.V. de Mello, C. Bloch Jr., L Morhy, J.B. Aragão and G. Neshich: "Determination of the disulphide bridges in 2S albumin from Brazil nut (Bertholetia excelsa H.B.K.) ". In "Programa e Resumos da XXII Reunião Anual da Sociedade Brasileira de bioquimica e biologia molecular” Caxambu, MG, Brazil 1-4 May, 1993.

8.14. L.H.Marcellino, E. Gander, A.S. Conceicao, E. Krebers and G. Neshich: "Introduction of tryptophan in the brazil nut 2s protein". In "Programa e Resumos da XXII Reuniao Anual da Sociedade Brasileira de bioquimica e biologia molecular" Caxambu, MG, Brazil 1-4 May, 1993.

8.15. S.M.Freitas, L.V.Mello, M.C.M.Silva, M.M.Ventura and G.Neshich: "The Binding Surface Identification Through The Homology Modeling For The System Black

Eyed Pea Trypsin And Chymotrypsin Inhibitor (BTCI)/Chymotrypsin". Caxambu, MG, Brazil,

May 14-17, 1994.

8.16. P.G.B.Carvalho, C.Bloch Jr. L.V.Mello, M.C.M. Silva, G.Neshich : "Calculation of Electrostatic Potential Around The Active Site Region For The System: Bowman-Birk Inhibitor From Seeds of Phaseolus vulgares Var. “Fogo na Serra” (PFSI) /Chymotrypsin". Caxambu, MG, Brazil, May 4-17, 1994.

8.17. E. Gander, M. Vicentz, A. Leite, M.C. Mattar de Silva, G. Vriend, L. Barros, D. Weinberg, E. R. de Almeida, M. Pais de Carvalho, F. Aragão and. G. Neshich:

"The opaque-2 regulatory protein recognizes acgt and vicilin core sequences in an essential seed specific promoter region from a brazil nut albumin  gen." The Protein Society - Ninth Symposium, Boston, MA - USA, July 8-12, 1995. PROGRAM & ABSTRACTS: 180 (672-M)

8.18. T.B. Cavalcante, A Rezende, R. Togawa and G. Neshich: " Field data collection, relational data-base data formating, printing of the data on the self- adhesive labels and data distribution through World Wide Web". XLVII Congresso Nacional de Botanica, Nova Friburgo/RJ, Brazil, 21-26 de Julho de 1996.

8.19. M.C. Mattar da Silva, G. Neshich, R. Togawa, M.Crispeels and M. F. Grossi de Sa: "Molecular Modeling of Plant alpha-amylase inhibitors and insect alpha-amylases complexes". III Encontro Latino Americano De Biotecnologia Vegetal, La Havana, Cuba, June 1-5, 1998

8.20. Da Silva MCM, G. Neshich, Ghrispeels M., Roberto Togawa and Grossi de Sa, M.F: "Molecular Basis of the Interactions Between InsectAlpha-Amylases and Inhibitors". XXVIII Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu, MG, Brazil,May 22-25, 1999.

8.21. Fonseca, A.S., G. Neshich, Brigido M.M.: "Design and Construction of a Humanized Version for the Ant-CD2 Fv through a New Strategy." XXVIII Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu, MG, Brazil, May 22-25, 1999.

8.22. Goran Neshich, Roberto C. Togawa, Wellington Vilella Torres, Tharsis Fonseca e Campos, Leonardo Lima Ferreira, Adilton Guedes Oliveira, Ronald Tetsuo Miura, Marcus Kiyoshi Inoue, Luiz Gustavo Horita, Georgios Pappas Jr.,Barry Honig: "STING Millennium: Web based suite of programs for comprehensive and simultaneous analysis of structure and sequence", ISMB 2001, Denmark, abstract#87

8.23. Adauto L. Mancini, Roberto H. Higa, Paula R. Kuser, Michel E. B. Yamagishi and Goran Neshich: "STING MILLENNIUM SUITE (SMS): a Web tool for identification and visualization of protein

intra and inter chain contacts", Resumo número: 301595. XXXII Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu, MG, Brazil, May 17-20,

2003.

8.24. Michel E. B. Yamagishi, Adauto Mancini, Roberto H. Higa, Paula R. Kuser and Goran Neshich:

"In Silico Filtering of Successful Protein-Ligand Binding", Resumo numero: 300345. XXXII Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu,

MG, Brazil, May 17-20, 2003.

8.25. Roberto H. Higa, Christian Baudet, Paula R. Kuser, Adauto L. Mancini, Michel E. B. Yamagishi

and Goran Neshich: "Java Protein Dossier – a java tool for analyzing stability and potential function of proteins with known structure", Resumo número: 300592. XXXII Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu, MG, Brazil, May 17-20, 2003.

8.26. Paula R. Kuser, Roberto H. Higa, Christian Baudet, Adauto L. Mancini, Michel E. B. Yamagishi

and Goran Neshich: "STING MILLENNIUM - Suite of  software tools for analysis of protein structures and summary of structure/function parameters", Resumo número: 300538. XXXII Reuniao Anual da Sociedade Brasileira de Bioquimica e Biologia Molecular - SBBq - Caxambu, MG, Brazil, May 17-20, 2003.

8.27. Goran Neshich, Roberto Togawa, Walter Rocchia, Adauto L. Mancini, Paula R. Kuser, Michel E. B. Yamagishi, Alexandre 301lvaro, Christian Baudet and Roberto H. Higa: "STING MILLENNIUM SUITE v.3 and JAVA PROTEIN DOSSIER: a novel concept in data visualization and analysis of the protein structure/function relationship" has been accepted for presentation at ISMB2003, Brisbane, Australia, 29th June - 3rd July, 2003.

8.28. Guelfi, A., Molina, S. M. G., Neshich, G.: "Structural alignment: A clue for enzyme function?", 49º Congresso Nacional de Genética - SBG - Águas de Lindóia, SP, Brazil, September 16 - 19, 2003.

8.29. Hernandez, J.F.1, Hayashi, M.A.F.2, Neshich, G., and Camargo, A.C.M.2 : " “in silico” model for human sACE substrate binding : structural parameters defining N- and C-domain substrate specificity", I São Paulo Research Conference : Molecular Medicine. Sao Paulo, Brazil, 2003.

8.30. Neshich, G. GRID Computing at EMBRAPA: "Searching for the best shape match between the potential drug targets at the protein surfaces and small chemicals"In: Workshop de Grade Computacional e Aplicações, LNCC, 2003. v.1. p.97 - 102, Petrópolis, RJ, Brazil, 2003.

8.31. Hernandez, J.F.1, Hayashi, M.A.F.2, Neshich, G.1, and Camargo, A.C.M.2: " Comparative Modelling of the N-terminal Domain of the Human Somatic ACE-Lisinopril Complex" - V Reunião Científica Anual do Instituto Butantan, Sã Paulo, Brazil, December 01- 05, 2003.

8.32. Neshich, Goran; Fernandez JH; Hayashi MAF; Camargo ACM: “IN SILICO” MODEL FOR HUMAN sACE SUBSTRATE BINDING: STRUCTURAL  PARAMETERS DEFINING N- AND C- DOMAIN SUBSTRATE SPECIFICITY". In: I SÃO PAULO RESEARCH CONFERENCE : MOLECULAR MEDICINE., 2003, SP. Anais de I São Paulo Research Conference : Molecular Medicine.. Brazil, 2003.

2004.

8.33. Neshich, Goran; GUELFI, Andrea; G, Molina S M: "Structural alignment: a clue for enzyme function". In: II ESCOLA DE MODELAGEM MOLECULAR EM SISTEMAS BIOLOGICOS, 2004, Petropolis: LNCC, Brazil, 2004.

8.34. Neshich, Goran; MANCINI, Adauto; HIGA, Roberto Hiroshi; KUSER, Paula; MICHEL, Yamagishi "Gold STING: the new DB and concept in protein structure/function data visualisation/analysis". In: SBBQ XXXIII, 2004, Caxambu. Brazil, 2004.

8.35. Neshich, Goran; MANCINI, Adauto; KUSER, Paula; FILETO, Renato; MICHEL, Yamagishi; HIGA, Roberto Hiroshi:

"Gold STING: studying protein stability and folding by looking at an extensive DB of the structure descriptors". In: ISMB 2004, 2004, Glasgow. ISMB 2004. Scotland, 2004.

8.36. Neshich, Goran; MANCINI, Adauto; KUSER, Paula; FILETO, Renato; MICHEL, Yamagishi; HIGA, Roberto Hiroshi: "Selecting a set of the protein structure descriptors uniquely defining the active site residues". In: 3D-SIG: ISMB 2004, 2004, Glasgow. ISMB 2004. Scotland, 2004.

8.37. HERNANDEZ, Jorge Fernandez; NESHICH, Goran; CM, Camargo Antonio.: "USING BRADYKININ POTENTIATING PEPTIDE (BPP) STRUCTURES TO DEVELOP NEW ANTIHIPERTENSIVE DRUGS". In: ICOBICOBI, 2004, Angra dos Reis. Brazil. 2004.

8.38. NESHICH, Goran; KUSER, Paula; JESUS, Katia Regina Evaristo de; MANCINI, Adauto; MICHEL, Yamagishi; RENATO, Fileto; ROBERTO, Higa.:         "The signals hidden in a set of protein structure descriptors: in silico identifying a protein active site". In: 1ST LATIN AMERICAN PROTEIN SOCIETY MEETING, 2004, Angra dos Reis. Brazil. 2004.

8.39. NESHICH, Goran; JESUS, Katia Regina Evaristo de; KUSER, Paula; MICHEL, Yamagishi; MANCINI, Adauto; RENATO, Fileto; ROBERTO, Higa.:        "Identifying a protein active site in silico by selecting for the signals hidden in a set of protein structure descriptors". In: ICOBICOBI, 2004, Angra dos Reis. Brazil. 2004.

8.40. NESHICH, Goran; MANCINI, Adauto; HIGA, Roberto Hiroshi; KUSER, Paula; MICHEL, Yamagishi.: Gold STING: the new DB and concept in protein structure/function data visualisation/analysis. In: SBBQ XXXIII, Brazil, Caxambu. 2004.

8.41. NESHICH, Goran; YAMAGISHI, M. E. B. ; ROCCHIA, Walter ; MANCINI, Adauto ; FALCÃO, Paula Regina Kuser ; FILETO, Renato ; BAUDET, Christian ; PINTO, Ivan ; MONTAGNER , Arnaldo ; PALANDRANI, Juliana ; KRAUCHENKO, João ; TORRES, Renato Cristiano ; BEZERRA, George Barreto Pereira   ; SOUZA, Sávio ;TOGAWA, Roberto C. ; HIGA, Roberto Hiroshi .: " Protein Structure Analysis and Visualization Using Java Protein Dossier". In: International Conference on Chemometrics and Bioinformatics in Asia, 2004, Shanghai. Proceedings of International Conference on Chemometrics and Bioinformatics in Asia, China, ,p. 128- 128.2004

2005.

8.42. KUSER, Paula; YAMAGISHI, Michel; MANCINI, Adauto; HIGA, Roberto; BORRO, Luiz C; NESHICH, Goran.: "STING - A web server for comprehensive analysis of protein structure and sequence". In: ISMB 2005, 2005, Detroit. USA ISMB proceedings. 2005

8.43. KUSER, Paula; YAMAGISHI, Michel; MANCINI, Adauto; BORRO, Luiz C; NESHICH, Goran.: "Identification of folding essential residues by looking at an extensive DB of the structure descriptors in Diamond STING". In: ISMB 2005, Detroit. USA ISMB 2005 proceedings. 2005.

8.44. Marcelo G. Narciso, Michel E. B. Yamagishi, Thiago Quinalia, George B. P. Bezerra, Goran Neshich.: "2D Maps of Protein Interface Surfaces". In: X-Meeting Brazil, Caxambu. 2005

8.45. Michel E. B. Yamagishi, George B. P. Bezerra, Thiago Quinalia, Paula R. Kuser, Roberto H. Higa, Adauto L. Mancini, José G. Jardine, Ivan Mazoni, Edgard H. dos Santos, Sérgio A. B. Cruz, Stanley R. M. Oliveira, Goran Neshich.: "An Interative Protein Interface Surface Java Viewer". In: X-Meeting, Brazil, Caxambu. 2005

8.46. Roberto Hiroshi Higa, Sergio Aparecido Braga da Cruz, Paula Regine Kuser, Michel Eduardo Beleza Yamagishi, Renato Fileto, Adauto Luiz Mancini and Goran Neshich.: "Building Multiple Sequence Alignments with a flavour of HSSP alignments". In: X-Meeting, Brazil, Caxambu. 2005

8.47. Sergio A. B. da Cruz, Ivan Mazoni, Stanley R. M. Oliveira, Michel E. B. Yamagishi, Paula R. Kuser, Edgard H. Santos, Fabio D. Vieira, Roberto H. Higa, Adauto L. Mancini, Goran Neshich.: "JMOL and STING integration: a STING for multiple plataform". In: X-Meeting, Brazil, Caxambu. 2005

8.48. Guelfi, A.; Chabregas, S. M.; Falco, M. C., Falcão, P. K., Neshich, G.; Azevedo R. A.; "Molecular Dynamics Analysis of Glutathione Transferases Sugarcane Mutants and Their Interactions With Atrazine". In: X-Meeting, Brazil, Caxambu. 2005

8.49. José G. Jardine, Goran Neshich, Paula R. K. Falcão, Michel E. B. Yamagishi, Stanley R. M. Oliveira, Sérgio Marangoni, Daniel Martins, Flavia V. Winck,José C. Novello.: "Molecular Modeling of the Protein Twitching Motility of Xylella fastidiosa". In: X-Meeting, Brazil, Caxambu. 2005

8.50. Mariana Simões, Diana Bahia, Kleider Torres, Adhemar Zerlotini Neto, François Artiguenave, Paula Kuser, Goran Neshich, Guilherme Oliveira.: "SNP Identification in Schistosoma mansoni Expressed Genes". In: X-Meeting, Brazil, Caxambu. 2005

8.51. Stanley R. M. Oliveira, Daniel S. Pavanelli, Gustavo V. Almeida, Michel E. B. Yamagishi, Paula

. Kuser, Edgard H. Santos, Fabio D. Vieira, Ivan Mazoni, Sergio A. B. da Cruz, Roberto H. Higa, Adauto L. Mancini, Goran Neshich.: "STING_DB: A relational database of structural parameters of protein analysis". In: X- Meeting, Brazil, Caxambu. 2005

8.52. Katia Regina Evaristo de Jesus, Paula Kuser Falcão, Goran Neshich. "Structural Analyses of Cry 1Ac Protein from Bacillus thuringiensis". In: X-Meeting, Brazil, Caxambu. 2005

8.53. Goran Neshich, Paula Kuser, Michel Yamagishi, Stanley Oliveira, Ivan Mazoni, Edgard Santos,

Favio Vieira, Sergio Cruz, Adauto Mancini, Jose Gilberto Jardine, Roberto Higa.: "What makes the active site amino acids so different from the others: defining the structural descriptors specific for activity". In: X-Meeting, Brazil, Caxambu. 2005

8.54. Noboru Furukawa, Yuko Takeno, Goran Neshich and Akinori Sarai.: " Systematic Analysis of Structure-Stability Relationship for Proteins and Mutants".

         In: The 16th International Conference on Genome Informatics, held at PACIFICO YOKOHAMA,

December 19-21, 2005., JAPAN, 2005.

8.55. Paula R. Kuser, Michel E. B. Yamagishi, Luiz C. Borro, Adauto Mancini, Roberto Higa and Goran Neshich.: "Identification of folding essential residues by looking at an extensive DB of the structure descriptors in Diamond STING". In: ISMB 2005, Detroit, USA. 2005

2006.

8.56. Stanley R. M. Oliveira, Diego N. Rodrigues , Kassyus R. R. Souza, Ivan, Gustavo V. Almeida, Paula R. K. Falcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José G. Jardine

and Goran Neshich; "STING Database Quality Assessment". In: ISMB 2006, Fortaleza. Brazil ISMB 2006         proceedings, Poster B-33. 2006

8.57. R.C. Melo, I. Mazoni, G. Neshich, M.M. Santoro and W. Meira Jr; "Contacts as the key elements for comparing two protein structures". In: ISMB 2006, Fortaleza.

Brazil ISMB 2006 proceedings - Poster I-6. 2006

8.58. R.C. Melo, I. Mazoni, G. Neshich, M.M. Santoro and W. Meira Jr; "Protein structure topology comparison based on contact maps". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-5. 2006

8.59. Michel E. B. Yamagishi, Paula R. Kuser1, Luiz C. Borro, Stanley Oliveira, Edgar H. Santos, José G. Jardine, Fábio D. Vieira, Ivan Mazoni and Goran Neshich;   "Analysing Protein-Protein Interface using the STING JPIV". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-14. 2006

8.60. Michel E. B. Yamagishi, Stanley Oliveira, Luiz C. Borro , Edgar H. Santos, José G. Jardine, Fábio D. Vieira, Ivan Mazoni, Paula R. Kuserand Goran Neshich; "Predicting Enzyme Class From Protein Structural Parameters Using STING_DB parameters and Bagging Predictors". In: ISMB 2006, Fortaleza. Brazil ISMB 2006proceedings, Poster I- 13. 2006.

8.61. José G. Jardine, Goran Neshich; Paula R. K. Falcão, Michel E. B.Yamagishi, Stanley R. M. Oliveira, Juliana M. Papine, Mariana S. Vieira; "Structural Analysis of proplasmepsin from the human malarial pathogen plasmodium vivax". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-34. 2006

8.62. Jorge Hernandez Fernandez, Vanessa Rioli, Emer S.Ferro, Fernanda C. Portaro, Antonio Carlos M. Camargo; "Dynamics of catalysis and inhibition in oligopeptidases: Natural peptide structures as promising antihypertensive agents". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster  E-8 . 2006

8.63.Paula R. Kuser, Michel E. B. Yamagishi, Stanley R. M. Oliveira, Ivan Mazoni Edgard H. Santos, Fábio D. Vieira, José G. Jardine Luiz C. Borro and Goran Neshich;

"BlueStar STING - A multiplatform environment for protein structure analysis". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-22. 2006

8.64. José G. Jardine, Goran Neshich; Paula R. K. Falcão, Michel E. B.Yamagishi, Stanley R. M. Oliveira, Ivan Mazoni, Edgard H. Santos, Fábio D. Vieira, Sérgio Marangoni; Daniel Martins; Flavia V. Winck; José C. Novello; "Structural Analysis of the Protein Twitching Motility of Xylella fastidiosa". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-35. 2006

8.65. Stanley R. M. Oliveira, Diego N. Rodrigues , Kassyus R. R. Souza, Gustavo V. Almeida, Goran

Neshich, Paula R. K. Falcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José G. Jardine; "An Integrated database of structural parameters for protein analysis". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster B-44. 2006

8.66. Katia Regina Evaristo de Jesus, Paula Kuser Falcão, Goran Neshich; "The Cry 1Ac Protein from Bacillus thuringiensis and its structure stability centers".         In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-47. 2006

8.67. Cristina Ribeiro, M.M. Santoro, Goran Neshich; "Serine Proteases analisys based on phylogenetic trees constructed from the sequence and structure alignments". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster LB-39 and I-48. 2006

8.68. Ivan Mazoni, Paula R. Kuser-Falcão, Michel E. B. Yamagishi, Luiz C. Borro, José G. Jardine, Edgard H. dos Santos, Stanley R. M. Oliveira, Goran Neshich;         "MSSP: simultaneous comparison of the same structure descriptor for different protein structures". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I- 50. 2006

8.69. Luiz C. Borro, Ivan Mazoni, Paula R. Kuser-Falcão, Michel E. B.Yamagishi, José G. Jardine, Edgard H. dos Santos, Stanley R. M. Oliveira, Goran Neshich;         "Protein Ligand Contacts Analysed In An Integrated Environment With Other Structure And Sequence Related Parameters". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I49. 2006

8.70. Marcelo Narciso, Ivan Mazoni, Paula R. Kuser-Falcão, Michel E. B. Yamagishi, José G. Jardine, Edgard H. dos Santos, Stanley R. M. Oliveira, Goran Neshich;         "Comparisson of AA co-evolution and correlated structure descriptors". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-51. 2006

8.71. Stanley R. M. Oliveira, Diego N. Rodrigues, Kassyus R. R. Souza, Gustavo V. Almeida, Goran Neshich, Paula R. K. Falcão, Michel E. B.Yamagishi, Edgard H. Santos, Fábio D. Vieira, José

G. Jardine; "Sting_RDB: A Relational Database of Structural Parameters for Protein Analysis". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Demo. 2006

8.72. Marcelo G. Narciso, Michel E. B.Yamagishi, Paula R. K. Falcão and Goran Neshich,: "2D Maps of Protein Surface". in: ISMB 2006, Fortaleza. Brazil ISMB 2006  proceedings, Poster B-63. 2006

8.73. Maria Cristina Mattar da Silva, Fabíola Rodrigues Teixeira, Cleiton C.M, da Cruz, Roberto Togawa, Goran Neshich and Maria Fatimaosé Grosse de Sá; "In vitro Molecular Expression of Bean Alpha-Amulase Inhibitors -Investigating Specificity of Binding to Alpha Amylases". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster

LB-28. 2006

8.74. Marcelo Mendes Brandão, Paula R. K. Falcão and Goran Neshich, "Structural Parameters to Filter Crucial Catalytic Site Amino Acids from Fructose 1,6-          Biphosphate Aldolase". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-21.

8.75. Marcos Tadeu Santos, Lucio Fabio Caldas Ferraz, Fernanda de Castro Reis, Ana Paula Felicio, Paula R. K. Falcão, Maria Teresa marques Novo, Goran Neshich, Oswaldo Garcia Jr, Laura Maria Mariscal Ottoboni; "Sequence Analysis of the Riboflavin Biosythesis Genes from Acidithiobacillus ferrooxidans". In: ISMB 2006,Fortaleza. Brazil ISMB 2006 proceedings, poster H-76. 2006

8.76. Lucio Fabio Caldas Ferraz, Fernanda de Castro Reis, Marcos Tadeu Santos,Ana Paula Felicio,

Paula R. K. Falcão, Maria Teresa marques Novo, Goran Neshich, Oswaldo Garcia Jr, Laura Maria Mariscal Ottoboni; "Molecular Modelling of the Riboflavin Genes from Acidithiobacillus ferrooxidans" In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-90. 2006

8.77. Fernanda de Castro Reis, Lucio Fabio Caldas Ferraz, Marcos Tadeu Santos, Paula R. K. Falcão, Goran Neshich and Laura Maria Mariscal Ottoboni; "Molecular Modelling of polypeptide deformylase from Acidithiobacillus ferrooxidans". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster I-95. 2006

8.78.Lucio Fabio Caldas Ferraz, Fernanda de Castro Reis, Paula R. K. Falcão, Goran Neshich and Maricilda Palandi de Melloi; "Molecular Homologous Modelling of 3B-HSD2 Mutant Enzyme: Structure-Function Aspects of PRO222GLN Mutation Correlates with the Experimental data from a Patient with Congenital        Adrenal Hyperplasia". In: ISMB 2006, Fortaleza. Brazil ISMB 2006 proceedings, Poster D-12.

2006

  8.79. Marcelo G. Narciso; Goran Neshich; Michel B.Yamagishi; Paula Falcão; Edgar Henrique; Fábio D.Vieira; José G.Jardine; Ivan Mazoni              " Aspectos computacionais da análise da co-evolução de aminoácidos que pertencem a uma proteína qualquer usando o software Sting". II Congresso de Computação do Sul de Mato              Grosso - COMPSULMT2006 16 a 20 de outubro de 2006 Rondonópolis, MT

   8.80. Marcelo G. Narciso;Michel B.Yamagishi;Goran Neshich; Paula Falcão; Edgar Henrique; Fábio D. Vieira; José G. Jardine; Ivan Mazoni

             "Transformação de imagens 3D para 2D para análise de proteínas usando o software Sting". II Congresso de Computação do Sul de Mato Grosso - COMPSULMT2006 16 a 20 de outubro              de 2006 Rondonópolis, MT

2007.

8.81.Luiz César Borro, Ivan Mazoni, Daniel Alvarenga, Thais Vital Pelligrinelli, Mauri Carvalho, José Gilberto Jardine and Goran Neshich; "Chameleon sequences seen under a prism of structure descriptors". In: X-meeting 2007, São Paulo. Brazil. X-meeting proceedings, Poster XP190. 2007

8.82. Ivan Mazoni, Luiz César Borro, Daniel Alvarenga, José Gilberto Jardine and Goran Neshich; "JavaSecondary Structure Dossier". In: X-meeting 2007, São Paulo. Brazil. X-meeting proceedings, Poster XP48. 2007

8.83.José Gilberto Jardine, Goran Neshich, Ivan Mazoni, Daniel Martins, Sérgio Marangoni, José Camillo Novello, Wagner F. Gattaz, Emmanuel Dias-Neto; "Molecular Homologous Modelling of 3B-HSD2 Mutant Enzyme: Structure-Function Aspects of PRO222GLN Mutation Correlates with the Experimental data from a Patient with Congenital Adrenal Hyperplasia". In: X-meeting 2007, São Paulo. Brazil. X-meeting proceedings, Poster XP40. 2007

8.84.Cristina Ribeiro, Marcelo Santoro, Goran Neshich; "Protein Dossier and Protein Fingerprints produce Surface Signatures: A simple and powerful technique for coding and comparing compound and receptor shape information". In: X-meeting 2007, São Paulo. Brazil. X-meeting proceedings, Poster XP 220. 2007

8.85.Raquel Melo, Janaína Gomide, Wagner Meira Jr., Júlio Lopes, Goran Neshich, Marcelo Santoro; "Mining Structural Signatures in Proteins using Intrachain Interactions". In: X-meeting 2007, São Paulo. Brazil. X-meeting proceedings, Poster XP15. 2007

2008.

8.86.Ivan Mazoni, Luiz César Borro, Daniel Alvarenga, Pablo Lira Cecilio, José Gilberto Jardine, Adauto Mancini and Goran Neshich; “Dossier of Secondary Structure Elements Amino Acid Properties”. In: ISMB 2008 July 18 to 23, Toronto. Canada.

8.87.Mazoni I., Borro L.C., Alvarenga D., Jardine J.G., Goran Neshich; “STUDYING STRUCTURE FUNC-TION RELATIONSHIP OF PROTEINS USING “REMEDIATED” PDB FILES ”. In: SBBq 2008 May 17 to 20, Águas de Lindóia. Brazil.

8.88. Mazoni I., Jardine J.G, Borro L.C., Alvarenga D., Goran Neshich; “ELECTROSTATIC POTEN-TIAL AT THE ALPHA CARBON ATOMS ALONG THE ALPHA HELICES AND BETA STRANDS ”. In: SBBq 2008 May 17 to 20, Águas de Lindóia. Brazil.

8.89. Jardine J.G., Mazoni I., Borro L.C., Alvarenga D., Goran Neshich; “SIGNATURE CONTACT CO-ORDINATION PATTERNS FOR SECONDARY STRUCTURE ELEMENTS IN PROTEIN STRUC-TURES ”. In: SBBq 2008 May 17 to 20, Águas de Lindóia. Brazil.

8.90. Jardine J.G., Mazoni I., Mancini A., Borro L.C., Alvarenga D., Cecilio P.L, Pelligrinelli T.V. and Goran Neshich; “HOW DID THE STRUCTURE FUNCTION DESCRIPTORS OF PROTEINS

CHANGE WITH INTRODUCTION OF "REMEDIATED" PDB FILES”. In: RIB 2008 October 15 to 17, Santiago. Chile.

8.91. Mancini A., Jardine J.G., Mazoni I., Borro L.C., Alvarenga D., Cecilio P.L, Pelligrinelli T.V. and Goran Neshich; “Structure Descriptors of Chameleon Sequences ”. In: RIB 2008 October 15 to 17, Santiago. Chile.

8.92. Borro L.C., Mazoni I., Alvarenga D., Cecilio P., Grassi, J.A., Mancini A., Jardine J.G. and Goran Neshich; “CONTACT COORDINATION PATTERNS AND ELECTROSTATIC POTENTIAL AT AL-PHA CARBON ATOMS: A DOSSIER OF PROTEIN SECONDARY STRUCTURE ELEMENTS”. In: EMBnet Conference 2008: 20th Anniversary Celebration,2008 September 18 - 20, Martina Franca (Puglia), Italy.

8.93. Izabella Pena ; MANCINI, Adauto L. ; MAZONI, Ivan ; JARDINE, Jose Gilberto ; Neshich, Goran ; José Miguel ortega . "Identification of phylogenetic relationship between GDPD and SMaseD proteins based on active site amino acid physical chemical properties". In: x-meeting, 2008, Salvador, BA. x-maating 2008, 2008, Brazil.

9. THESIS COMMITTEE PARTICIPATIONThis Section Updated: JANUARY 14, 2009

9.1.1. "Disulphide bridge determination in 2S albumin from Brazil nut (Bertholetia excelsa H.B.K.)9.1.2. author: Maria Cristina Mattar da Silva9.1.3. degree: Msc, UnB - Brasilia, Brazil9.1.4. participation: thesis adviser9.1.5. Finalized: 1993

9.2.1. "Purification and the partial amino-acid sequence of the tripsin- chymotripsin inhibitor from the Dolichos labiab cv albiflorus seeds"9.2.2. author: Marcelo Silveira de Alcantra9.2.3. degree: Msc, UnB - Brasilia, Brazil9.2.4. participation: committee member9.2.5. Finalized: 1994

9.3.1. "Secondary structure prediction of the globular proteins: structure prediction software design - COMBO, and its utilization for the analysis of the C-terminal region of the proteins binding to poly-A (PABP)”9.3.2. author: Antonio Francisco Pereira de Araújo9.3.3. degree: Msc, UnB - Brasilia, Brazil9.3.4. participation: committee member9.3.5. Finalized: 1994

9.4.1. "Structural analysis of Piruvate Decarboxilase from Saccharomyces cerevisiae"9.4.2. author: Maria Angela Lopes de Almeida Arrazonas9.4.3. degree: Ph.D., UNICAMP - Campinas, Brazil9.4.4. participation: committee member9.4.5. Finalized: 1994

9.5.1. "Trypsine and Chymotrypsine inhibitor from Vigna unguiculata (L.) Walp: Modeling of three dimensional structure by homology, Thermodynamics and Kinetics of the interaction with a-Chymotrypsine"

9.5.2. author: Sonia Maria de Freitas9.5.3. degree: PhD., UnB - Brasilia, Brazil9.5.4. participation: committee member9.5.5. Finalized: 1995

9.6.1. "Inibidores de Proteinase do Tipo Bowman-Birk: Evolução Molecular, Expressão na Superfície de Fagos Filamentosos e seu Papel na Interação Planta-Inseto"9.6.2. author: Marcia Ometto de Mello Alves José9.6.3. degree: PhD., ESALQ/USP, Piracicaba, Brazil9.6.4. participation: committee member9.6.5. Finalized: 2002

9.7.1. "Structure Function Relationship for Glutationa S transferase proteins "9.7.2. author: Andrea Guelfi9.7.3. degree: PhD., ESALQ/USP, Piracicaba, Brazil9.7.4. participation: committee member9.7.5. Finalized: 2006

9.8.1. "In Silico analysis of the patterns in interactions established between the serion proteases and their inhibitors"9.8.2. author: Cristina Ribeiro9.8.3. degree: PhD., UFMG, Belo Horizonte, Brazil9.8.4. participation: co-advisor9.8.5. Finalized: in progress

9.9.1. "Globulins and their internal contact motifs analysed togather with other structure descriptors"9.9.2. author: Carlos Henrique da Silveira9.9.3. degree: PhD., UFMG, Belo Horizonte, Brazil9.9.4. participation: co-advisor9.9.5. Finalized: 2008

9.10.1. "Predicting hydrogen atom positions in proteins using neural networks"9.10.2. author: Adauto Luiz Mancini9.10.3. degree: MSc., UFSCAR, Sao Carlos, Sao Paulo, Brazil9.10.4. participation: co-advisor9.10.5. Finalized: 2008

9.11.1. "Protein classification based on internal contact patterns"9.11.2. author: Raquel Melo9.11.3. degree: PhD., UFMG, Belo Horizonte, Brazil9.11.4. participation: co-advisor9.11.5. Finalized: 2008

9.12.1. "TargetsDB - Base de dados de alvos terapêuticosvalidados"9.12.2. author: Eduardo Campos dos Santos9.12.3. degree: PhD., UFMG, Belo Horizonte, Brazil9.12.4. participation: co-advisor9.12.5. Finalized: in progress

9.13.1. "Meio ambiente dos elementos da estrutura secondaria em proteinas."9.13.2. author: Ivan Mazoni9.13.3. degree: MSc., UNICAMP, Campinas, Brazil

9.13.4. participation: advisor9.13.5. Finalized: in progress

9.14.1. "Predição de epitopos em LiD1, proteína dermonecrotica do veneno da aranha marrom Loxosceles intermédia por bioinformática e Imonologia molecular"9.14.2. author: Ricardo Andrez Machado de Ávila9.14.3. degree: PhD., UFMG, Belo Horizonte, Brazil9.14.4. participation: co-advisor9.14.5. Finalized: in progress

9.15.1. "Desenvolvimento de Interface Web para Docking Automático de Consenso. "9.15.2. author: Andrelly Martins Jose9.15.3. degree: PhD., UFMG, Belo Horizonte, Brazil9.15.4. participation: co-advisor9.15.5. Finalized: in progress

9.16.1. "Estudos de comunicação entre as macromoleculas em homo e hetero complexos atraves das interfaces. "9.16.2. author: Fábio Rogéio de Moraes9.16.3. degree:PhD., UNICAMP, Campinas, Brazil9.16.4. participation: advisor9.16.5. Finalized: in progress

9.17.1. "Produção de um inibidor para Quinase de Adesão Focal (FAK) estudos estruturais"9.17.2. author: João Eustáquio Antunes9.17.3. degree:PhD., UNICAMP, Campinas, Brazil9.17.4. participation: co-advisor9.17.5. Finalized: in progress

9.18.1. "Produção de um compsto quimico simples, substituto de peptídeo natriurético, o inibidor de receptores do tipo Guanilato Ciclase."9.18.2. author: Álisson Campos Cardoso9.18.3. degree:PhD., UNICAMP, Campinas, Brazil9.18.4. participation: co-advisor9.18.5. Finalized: in progress

9.19.1. "Analise dos aspectos estruturais dos inibidores vegetais de enzymas proteoliticas."9.19.2. author: Vanessa da Silveira Ramos9.19.3. degree:PhD., UNICAMP, Campinas, Brazil9.19.4. participation: co-advisor9.19.5. Finalized: in progress

9.20.1. "Aspectos estruturais da atividade de um inibidor do tipo Kunitz de Adenanthera pavonina (APTI)"9.20.2. author: Desiree Soares da Silva.9.20.3. degree:PhD., UNICAMP, Campinas, Brazil9.20.4. participation: co-advisor9.20.5. Finalized: in progress

10. SOFTWARE PACKAGES PUBLISHED

All packages are available at:

Country www addressHome (Embrapa/CNPTIA, Campinas - Brazil) http://www.cbi.cnptia.embrapa.brUSA: PDB/RCSB at SCSD-UCSD http://mirrors.rcsb.org/SMSUSA: Columbia University http://trantor.bioc.columbia.edu/SMS/Spain: CNB-Madrid http://www.es.embnet.org/SMS/Japan: Kyushu Institute of Technology (KIT) http://gibk26.bse.kyutech.ac.jp/SMS/Argentina: La Plata http://www.ar.embnet.org/SMS/Brazil: Embrapa-Cenargen-Brasilia http://asparagin.cenargen.embrapa.br/SMS

10.1. STING---STING is a WWW tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). Special attention is given to MacroMolecular INTERFACE analysis. (1998)

10.2. STING_PAINT---STINGpaint is WWW tool for - sequence and multiple sequence alignment coloring - residue/nucleotide within_the_sequence_number identification - characterization of the immediate environment for any residue/nucleotide within the sequence. (1998)

10.3. HORNET---HORNET Specifically shows Hydrogen Bond Net formed between two protein chains (or protein and DNA). HORNET also shows exact listing of the Interface Forming Residues (IFR), based

on calculated buried surface area. (1998)

10.4. MDB_MINING---Molecular Data Base - MDBMining: is a compilation of a variety of algorithms for retrieving specific data from Protein Databank (PDB), SwissProt and GenEMBL. Total Residue/Nucleotide occurrence in each database, keyword search, file sizes, number of chains, resolution of 3D data, protein families classification are all available in MDBMining. (1999)

10.5. PDB_MINING---Protein Data Base - PDBMining: is a compilation of a variety of algorithms for retrieving specific data from Protein Databank (PDB). Total Residue occurrence in whole PDB, keyword search, file sizes, number of chains, resolution of 3D data, protein families classification are all available in PDBMining. (1999)

10.6. SCORPION---SCORPION is the WWW tool for analysis of the amino acid frequences within protein chain(s) (of given pdb file or group of pdb files) as well as foranalysis of 3D contacts of C-alpha and/or Last Hevy Atoms in the residue side chain (LHA). Convinient Graphical presentation can be used for identification of specific interactions for given family of the proteins or given domains. (1999)

10.7. FORMIGA---FORMIGA is a program that evoluted from SCORPION and is a WWW tool for analysis of PROTEIN INTERFACES with respect to amino acid residue frequences (of given pdb file or group

of pdb files) as well as for analysis of 3D contacts of C-alpha and/or Last Hevy Atoms in the residue side chain (LHA) for Interface Forming Residues (IFR). Convinient graphical presentation of calculated parameters makes possible to see specific interactions on the Protein Interfaces. (1999)

10.8. HESPER---HESPER: A tool for the analysis of homologous protein families derived from the HSSP database. (2000)

10.9. SPIDER---Serine Protease super-family Interface Data Resource (SPIDER) is an expanding collection of sequence, structural and functional information about the Serine Proteases Interface Forming Residues located around Active Site. (2000)

10.10. EMA---Evaluation of Multiple Alignments: A Comparison of Phylogenetic trees based on sequence alignments and structure alignments. EMA is a Data Resource available over WWW. (2000)

10.11. Ramachandran Plot -- Intelligent graphical presentation of the Ramachandran Plot using all advantages of Java programming language; Options allow inter connection of data in dihedral angle plot with 3D structure of the molecule. A number of subsets among amino acids can be highlighted for better correlation among 3D structure position and Psi/Pfi spot. (2000)

10.12. Protein Dossier -- This service provides a graphical report of several important structural characteristics of the PDB entry. It offers a plot from PDB cartoon annotated with color coded scales representing for each amino acid the corresponding temperature factor, solvent accessibility of the chain in isolation and in complex with the other present chains in PDB file, sequence conservation in a multiple alignment (relative sequence entropy) and histograms representing the atomic contacts (as in the Graphical contacts module), as well as IFR residue identification and IFR contacts. In addition, comparison of the Secondary Structure annotated by PDB and by DSSP is presented. (2000)

10.13. PDB_Cartoon -- Image of the amino acid sequence along with the secondary structure elements rendered as cartoons. (2000)

10.14. Contacts -- The atomic contacts between amino acids in a PDB entry received a special attention. The complete profile of the interactions can be analyzed in the graphical contacts window, which displays the primary sequence of a chain and below it a histogram containing the number of contacts

made by the respective residue. Virtual contact line connects residue of interest with other ones in contact with it, in a form of fan. This presentation is very intuitive and user can easily grasp contact parameters along the protein sequence. In case of IFR contacts, IFR are underlined with red line for easy identification. (2000)

10.15. ConSSeq -- This service presents PDB file sequence and consensus sequence (as found in HSSP) colored by conservation, color coded graphic bars of relative entropy, information about residues present in other homologous sequences, with their respective frequency. For fast visualization, this program generates the sequence logo. (2000)

10.16. Java Ca-Ca Distance plot -- is a diagram where the distances between the alfa carbon of one residue and all alfa carbon atoms of other residues, within a single chain of the PDB file, are represented by colored squares in a symmetrical plot. (2001)

10.17. Java Cb-Cb Distance plot -- is a diagram where the distances between the beta carbon of one residue and all beta carbon atoms of other residues, within a single chain of the PDB file, are represented by colored squares in a symmetrical plot. (2001)

10.18. Java MSA -- SMS_MSA stands for the new SMS component: Multiple Sequence Alignment. Those sequences are extracted both from HSSP and from our own SH2Qs (Sequences Homologue to the Query [Structure-having] Sequence). The latter one is designed so that we can benefit from the possibility of making a choice of the number of sequences that we want to consider in the relative entropy calculation. SMS_MSA will use standard MSA viewer package: SeaView. (2001)

10.19. Java Protein Dossier -- is a interactive presentation of important physical-chemical characteristics of the macromolecular structure described in PDB file. With a few mouse clicks the user can access data about chosen parameter, call other SMS modules or refine the search for a specific characteristics. By using color code scales for each residue of the sequence, JPD shows corresponding: temperature factor, solvent accessibility of the single chain (and also in complex with the other present chains in given PDB file), hydrophobicity, sequence conservation in a multiple alignment (relative entropy), double ocupancy, reliability and histograms representing the atomic contacts. JPD also shows the identification of Interface Forming Residue (IFR) and their internal contacts. JPD offers information about electrostatic potential and curvature on protein surface. In addition, comparison of the Secondary Structure annotated by PDB, by DSSP and by Stride is presented. (2002)

10.20. Java Table of Contacts -- is a interactive tool for listing contacts between residues of one protein and dividing them in specific classes. JTC shows all contacts for a specified residue, IFR Contacts and also Protein-DNA Contacts (the latter one starting from SMS version 3.1). This interactive tool allows user to access other SMS components or have physical-chemical parameters already "painted" within the table, such as: relative entropy, accessibility, secondary structure and the distance for the identified contacts. The user can make a choice of the resudes important for his consideration, make them appropriately displayed and then print the table of publication quality. (2002)

10.21. Protein DNA Contacts -- This SMS component demosntrates relevant contacts being established across the interface formed by protein and DNA chain. Similar logistics is used here as in IFR Graphical Contacts. (2003)

10.22. SMS_P3 -- SMS_P3 sands for SMS Phylogenetic Tree component. Phylogenetic tree is generated starting from either HSSP or SH2Qs multiple sequence alignments. TreeView standard viewer package is used to present to a user calculated phylogenetic trees. (2003)

10.23. SMS 2.2 -- STING Millennium is a new Java-based WWW tool for the simultaneous display of

information about macromolecular structure (in STING Millennium Graphics Window) and sequence (in STING Millennium Sequence Window). Includes graphical amino acid Contacts, Ramachandran plot, Surfaces, Sequence neighbors and other features. Parsing of data from relevant Data Bases (HSSP and SwissProt) is one of the key features of this integrated environment for structure/function analysis of the proteins, DNA and their complexes. To see the 3D structure you need to download and install the CHIME plugin. (2003)

10.24. Gold STING-- STING Millennium is a new Java-based WWW tool for the simultaneous display of information about macromolecular structure (in STING Millennium Graphics Window) and sequence (in STING Millennium Sequence Window). Includes graphical amino acid Contacts, Ramachandran plot, Surfaces, Sequence neighbors and other features. Parsing of data from relevant Data Bases (HSSP and SwissProt) is one of the key features of this integrated environment for structure/function analysis of the proteins, DNA and their complexes. To see the 3D structure you need to download and install the CHIME plugin. (2003)

10.25. STING Report -- GOLD STING Report is a web based application for extracting concise and focused information from the GOLD STING Data Base on specific amino acids within the structures described in PDB files. The extracted information is presented to a user through a series of GIF images and a table of numerical values for the set of structure/function descriptors/parameters, generated by the GOLD STING components. The resulting HTML page with the GIF images and the table is ready to be printed and most importantly, it can be visualize at platforms with the most elementary configurations (no java, chime, plug-ins etc.). Below is a schematic view of GIF image panels which are generally produced by the GOLD STING Report. We have used 1cho.pdb, chain E,

residue HIS_57 to generate GOLD STING Report for this help. Other panels will be added with the time, making GOLD STING Report GIF image collection more extensive. (2003)

10.26. Diamond STING -- Diamond STING is a new version of the STING suite of programs for comprehensive analysis of a relationship between protein sequence, structure, function and stability. We have added number of new functionalities by both providing more structure parameters to the STING Database and by improving/expanding the interface for enhanced data handling. The integration among the STING components has also been improved. A new key feature is the ability of the STING server to handle local files containing protein structures (either modeled or not yet deposited to the PDB) so that they can be used by the principal STING components: JavaProtein Dossier and STING Report. (2004)

10.27. Multiple Structure - Single Parameter (MSSP) 2D Plot - The Multiple Structures - Single Parameter 2D module allows the user to compare, in a graphical manner, any one of the 150 different parameters in different protein structures in a simple yet intuitive plot. The plot shows the numerical values in the Y-axis and the sequence residue numbers in the X-axis. (2006)

10.28. Contact Distance Map - Contact Distance Map (CDM) is a STING's module. It is designed to display graphically all the protein's contacts. Moreover, the Secondary Structure (SS) elements are also shown in a single line, facilitating theirs visualization for each residue, and contour curves distances maps involving a carbon, ß carbon and LHA-LHA (Least Heavy Atom) are presented in a Java interactive interface. (2006)

10.29. Protein Contacts Difference - In STING_PCD users can obtain a complete comparison report of the intrachain interactions for any two chains described in the PDB format file. The user must supply any two PDB ids and corresponding chain ids for the analysis. At the output, a user will receive a list of interactions which were preserved in both chains as well as the list of those which are present in only one of them. Users can also analyse a wild type protein and a corresponding mutant structure with a single point mutantion; in this case a user needs to supply at the input, the mutated amino acid name and the number. (2006)

10.30. Topology Similarity Map (TopSiMap) - STING_TopSiMap is a module which makes possible to compare the contact maps of two chains in terms of the preserved interactions as well as the ones which are present in only one of the two chains analysed. Users can see / print the images of the maps and also view the contacts in a JMol window where STING presents two structurally aligned chains. Users can also compare the chains in terms of the contacts classification (hydrophobic, aromatic stacking, hydrogen bonds, salt bridges and cysteine bridges) and corresponding energies. (2006)

10.31. STING_DB QA - This module is designed for checking the quality of STING_DB, the STING_DB Quality Assessment (STING_DB QA). With this new module, a user can perform the tracking of the PDB files which contains the insufficient information clarity for a specific structure descriptor calculation. Also, the overall quality of the STING_DB is much easier to assess now, setting this STING version apart from other products in this area. (2006)

10.32. STING_TGZ - STING_TGZ module generates a compressed file containing all the files used by several STING's modules, for example, JPD (Java Protein Dossier). These files are saved in different directories within the compressed file. If your research project needs to analyze the same pdb file very often, the best way to save time (in downloading data from internet) is to use STING_TGZ module. (2006)

10.33. 3D Java Protein Interface Viewer - JPIV - JPIV is a module of STING suite. It is designed to visualize and analyze the proteins' interfaces. In order to accomplish this, the interfaces are displayed separately, and over each one of them is painted a common physical-chemical property, available from STING_DB, that could be important in the complex formation. The contact interfaces are generated using weighted Delaunay triangulation and marching tetrahedra algorithms from the CGAL library, afterwards they and rendered in an Interactive Java Viewer based on JavaView library.

(2006)

10.34. PDB_Metrics - PDB Metrics can retrieve specific data from the Protein Data Bank (PDB). It provides

residues occurrences in the whole PDB repository, keywords search, PDB sorted by file size, PDB sorted by number of chains, PDB sorted by resolution of 3D data, protein families classification, among other facilities. (2006)

10.35. Star STING - Star STING is the February, 2006 version of the STING suite of programs and

corresponding database. Five important aspects of this package that acquired some new characteristics, designed to add key advantages to the whole suite: 1) Availability for most popular platforms and browsers, 2) Introduction of the STING_DB quality assessment, 3) Improvement in algorithms for calculation of three STING parameters, 4) Introduction of five new STING modules, and 5) expansion of the existing modules. The Star STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/ and http://trantor.bioc.columbia.edu/SMS. (2006)

10.36. 2-Dimensional Interface Maps - 2DIM - Designed to visualize separately the protein interfaces and analyze the main forces involved in protein complex formation. The 2DIM uses Floater's shape preserving algorithm to project the 3D protein interfaces into 2D, where it is then possible to superimpose the surfaces and estimate the interaction area between them. (2006)

10.37. Sting Enzyme Classification - Module dealing with a protein classification based on STING_DB parameters. (2006)

10.38. Topologs 100 - In this module, users can obtain the index for a toplogy similarity for a list of up to 100 structures. By submitting the STING TGZ file (containing all STING_DB parameters, precalcualated, corresponding to certain public or local structure) and a text file containing the list of up to 99 public PDB files, user can start the procedure which calculates the similarity index among selected (up to) 100 structures. This index is a reliable measure of the changes in the pattern of the intrachain interactions and can be used to analyse the topology similarities. (2006)

10.39. Topologs Astral 40 - This is a database of homologous PDB chains based on their interactions (contacts) pattern. For each of the "ASTRAL 40" ensamble chains, we computed a list of the most similar chains based on their contact maps. The database is searchable and for each chain, the list of the topologs is presented. (2006)

10.40. Multiple Parameter Aligment 3D Plot - Deals with the presentation of a single parameter for multiple structures or multiple parameters for a singles structure. (2006)

10.41. Amino Acid Co-evolution - The AA Co-evolution is the STING component which permits a user to examine co-evolution parameter of residues in a simple, yet intuitive 3D plot. A user may confirm which amino acid positions were identified by STING, within the previously confirmed amino acid conserved set, as evolved in concert. (2006)

10.42. Protein Ligand COntacts - This STING module can analyze the interatomic contacts in protein - ligand complexes. The contacts shown by this STING module include those mediated by charge- charge interactions, hydrogen bonds and hydrophobic contacts. (2006)

10.43. BlueStar STING - BlueStar STING is the July, 2006 version of the STING suite of programs and corresponding database. Five important aspects of this package that acquired some new characteristics, designed to add key advantages to the whole suite: 1) Relational Database of STING

parameters, 2) Amino acid co-evolving residues identified, 3) protein ligand contacts now available, 4) Sting Report now available in PDF format, and 5) improoved cross-talk among existing STING modules . The BlueStar STING is freely accessible at: http://sms.cbi.cnptia.embrapa.br/SMS/ and http://trantor.bioc.columbia.edu/SMS. (2006)

10.44. Java Secondary Structure Dossier (JSSD) - With this STING module a user may visually and numerically observe and analyze per residue reported structure descriptors for the SSE: alpha helices and beta strands. (2007)

11. SEMINARS & LECTURES GIVEN 1993

11.1."Bioinformatics: Databases and Computer Networks in Biology", 13 - 17 December 1993, REDBIO, Brasília, DF, Brazil. 1994

11.2."Bioinformatics: Databases and Computer Networks in Biology", 30 May - 03 June 1994, Held at the Fundação Tropical de Pesquisas e Tecnologia "André Tosello", Campinas, SP, Brazil. 1995

11.3.1. "Aperfeiçoamento em Biossegurança", 25 September - 25 Octuber 1995, Fundação Oswald Cruz FIOCRUZ, Rio de Janeiro, Brazil.11.3.2. "Workshop Internacional sobre Redes de Informação para Recursos Genéticos utilizando a Internet", 06 - 10 November 1995, Centro Nacional de Pesquisa de Recursos Genéticos e Biotecnologia - CENARGEN/EMBRAPA, Brasília, DF, Brazil.11.3.3. "Ecoturismo Científico mostrado pela Internet", November, 16 1995, Seminário da Amazônia 95, Manaus, AM, Brazil.

   199911.4.1. "Pragas quarentenárias: detecção e identificação", 07 - 11 June 1999, Centro Nacional

de Pesquisa de Recursos Genéticos e Biotecnologia CENARGEN/EMBRAPA, Brasília, DF, Brazil.   2001

11.5.1. "Bringing Genome Into Three Dimensions", March, 29 2001, Centro de Biologia Molecular do Laboratório Nacional de Luz Síncrotron, Campinas, SP Brazil.11.5.2. "Bringing Genome Into Three Dimensions", June, 26 2001, Instituto de Química da USP,

São Paulo, Brazil.11.5.3. "Bringing Genome Into Three Dimensions", August, 30 2001, Centro de Biologia Molecular e Engenharia Genética da UNICAMP, Campinas, SP, Brazil.11.5.4. "Bringing Genome Into Three Dimensions", September, 27 2001, Instituto Nacional de Pesquisas Espaciais, São José dos Campos, SP, Brazil.11.5.5. "Bioinformática - Experiências nos Últimos Meses", Octuber, 09 2001, Centro Nacional

de Pesquisa Tecnológica em Informática para a Agropecuária CNPTIA, Campinas, SP, Brazil.11.5.6. "Bioinformática: Bringing Genome Into Three Dimensions", November, 20 2001, Centro de Informática da UFPE, Recife, PE, Brazil.11.5.7. "Bioinformática: Definição, Limites e Oportunidades", Octuber, 08 2001, Centro Superior

de Educação Tecnológica, Limeira, SP, Brazil.11.5.8. "Bioinformática: Bringing Genome Into Three Dimensions", November, 11 2001, Laboratório de Computação Científica - LNCC/MCT, Petrópolis, RJ, Brazil.11.5.9. "Bringing Genome Into Three Dimensions", 03 - 08 December 2001, Instituto de Ciências Matemáticas e de Computação da USP, São Carlos, SP, Brazil.

   200211.6.1. "Bringing Genome Into Three Dimensions", April, 02 2002, Pontifícia Universidade Católica do Rio de Janeiro PUC-Rio, Rio de Janeiro, Brazil.11.6.2. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", April, 17 2002, NCBI: Department of Health& Human Services, USA.11.6.3. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", April, 26 2002, Columbia University, New York, NY, USA.11.6.4. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", May, 01 2002, University of California, San Diego, USA.11.6.5. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing

compound and receptor shape information", June, 04 2002, Laboratório de Computação Científica - LNCC/MCT, Petrópolis, RJ,Brazil.11.6.6. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", May, 28 2002, Instituto Butantan, São Paulo, SP, Brazil.

11.6.7. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", June, 14 2002, Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brazil.11.6.8. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", June, 07 2002, Centro de Informática da UFPE, Recife, PE, Brazil.11.6.9. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", August, 30 2002, Departamento de Genética ESALQ/USP, Piracicaba, SP, Brazil.

11.6.10. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", September, 16 2002, Universidade Federal de São Paulo UNIFESP/EPM, São Paulo,SP, Brazil.11.6.11. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", September, 19 2002, Instituto de Química de São Carlos da USP, São Carlos, SP, Brazil.11.6.12. "Recognition at macromolecular interfaces: Protein Dossier and Protein Fingerprints produce Surface Signatures, a simple and powerful technique for coding and comparing compound and receptor shape information", November, 21 2002, Faculdade de Ciências Farmacêuticas de Ribeirão Preto- USP,Ribeirão Preto, SP, Brazil.11.6.13. "Trazendo o Genoma em Terceira Dimensão", November, 29 2002, Instituto de Biologia da UNICAMP, Campinas, SP, Brazil.11.6.14. "Recognition at Macromolecular Interfaces", November, 26 2002, Centro Nacional de Pesquisa Tecnológica em Informática para a Agropecuaria CNPTIA, Campinas, SP, Brazil.

    200311.7.1. "Grid Computing and Chemogenomics", 27 - 31 January, in Workshop de Grade Computacional & Aplicações - LNCC, Rio de Janeiro, RJ, Brazil.11.7.2. "Structural Bioinformatics and The ISCB and de ISMB 2006 in Fortaleza", 17 - 19 March 2003, Reunión Preparatoria Red Iberoamericana de Bioinformática - SeCyT, Buenos Aires, Argentina. 11.7.3. "STING" at "Introdução à Biologia Computacional", 13 May 2003, Centro Brasileiro- Argentino de Biotecnologia - Hemocentro de Ribeirão Preto, Ribeirão Preto, SP, Brazil.11.7.4. "Bioinformatics from Genoms to Drugs", Simpósio 14 - 04, "Recognition at Macromolecular Interfaces: Protein Dossier Maps Surface Signatures and Physico Chemical Parameters Defining Binding Specifithy", 19 May 2003, SBBq 2003, Caxambu, MG, Brazil.11.7.5. "New features of SMS v.3 and Java Protein Dossier", PDB, 23 June 2003, San Diego, USA. 11.7.6. "STING Millennium Suite structure and function descriptors: a new addition to the existing jazz", 26 August 2003, Alellyx - Applied Genomics, Campinas, SP, Brazil.11.7.7. "Estudo de Relação entre Sequência e Estrutura das Proteínas e DNA", 30 September 2003, Faculdade de Informática Biomédica - USP, Ribeirão  Preto, SP,Brazil.11.7.8. "Sting Millennium Suite", 06 - 10 Octuber 2003, CNRS, Nancy, France.11.7.9. "Structural Bioinformatics", 27 Octuber 2003, Universidad de Talca - Facultad de Ingenieria, Chile.11.7.10."Opportunities and Challenges for Structural Bioinformatics", 30 Octuber 2003, Universidad de Talca - Facultad de Ingenieria, Chile.11.7.11."Tasks While Establishing Structural Bioinformatics Laboratory", 30 Octuber 2003, Universidad de Talca - Facultad de Ingenieria, Chile.11.7.12."High Performance Computing at Embrapa: searching for the best shape match between the potential drug targets at the protein surface and the small chemical compunds" Forum de Technologias e Aplicações de Sistemas de Alto Desempenho (FSAD2003), São Paulo, Brazil, November 10-12, 2003.11.7.13. "Opportunities and Challenges in Structural Bioinformatics - Searching for New Drugs" CAT-CEPID, Instituto Butantan, São Paulo, Brazil, November 19, 2003.

     2004

11.8.1. "Drug design and structural Bioinformatics", Knowledge Discovery in Genomic Databases, Pan American Advanced Studies Institute (PASI), February 12, 2004, Montevideo, Uruguay.11.8.2. "New features of Gold STING and JavaProtein Dossier" Knowledge Discovery in Genomic

Databases, Pan American Advanced Studies Institute (PASI), February 12, 2004, Montevideo, Uruguay.11.8.3. "Drug specific applications for the Gold STING, JavaProtein Dossier, and STING Report: case study - serine proteases" Knowledge Discovery in Genomic Databases, Pan American Advanced Studies Institute (PASI), February 16, 2004, Montevideo, Uruguay.11.8.4. "New Challanges and Opportunities for Structural Bioinformatics" Knowledge Discovery in Genomic Databases, Pan American Advanced Studies Institute (PASI), February 16, 2004, Montevideo, Uruguay.11.8.5. " Gold STING: Studying protein stability and folding by looking at an extensive DB of the Structure Descriptors" Programma de Seminarios em Biologia Computacional;Faculdade de Ciencias Farmaceuticas Riberao Preto USP, Brazil, Abril,

2004.11.8.6. " Gold and DIamond STING: The volume and quality of results 3 and 1/2 years after initiating the activities"; EMBRAPA Technical Meeting;Campinas, SãoPaulo, Brazil, May, 2004.11.8.7. "Protein Dossier - a Data Base of Physical-Chemical Parameters Describing Protein Function. 2004. Caxambu;Brazil, XXXIII SBBq; May, 200411.8.8. "GOLD STING - data base of protein structure and function describing parameters". Instituto de Biosciencias; Sao Jose do Rio Preto- Brazil; I Semana da Pos-Graduação em Biofisica Molecular; UNESP, June, 2004.11.8.9. " Opportunities and Challenges for Structural Bioinformatics". ; São Paulo-Brazil; Instituto de Quimica - USP. June, 200411.8.10. "Challages and Opportunities for Structural Bioinformatics". . Fortaleza - Brazil: WORKSHOP INTERNACIONAL DE NANOTECNOLOGIA APLICADA ÀS CIÊNCIAS BIOLÓGICAS;: UFCE. June, 200411.8.11. " Protein structure / function /binding descriptors: Gold STING". ; CNB - Madrid - Spain;July, 2004 .

11.8.12. "Protein structure / function /binding descriptors: Gold STING". Scuola Normale Superiore. Pisa- Italy; July, 2004.

11.8.13. "Protein structure / function /binding descriptors: Gold STING". ; ISMB-2004,Glasgow - Scotland; August, 2004. 11.8.14. "Protein structure / function /binding descriptors: Gold STING". ; CNRS, Nancy - France; August, 2004. 11.8.15. "Protein structure / function /binding descriptors: Gold STING". ;ZBH Zentrum für Bioinformatik, Hamburg -Germany; August, 2004. 11.8.16. "Protein structure / function /binding descriptors: Gold STING".Technical University of Denmark,Center for Biological Sequence Analysis, Biocentrum-DTU ;Copenhagen -

Denmark; August, 2004. 11.8.17. "Protein structure / function /binding descriptors: Gold STING". Center for Multidisciplinary Studies; Beograd -Yugoslavia; August, 2004. 11.8.18. "Genoma e Bioinformatica". In : 2a semana de atividades integradas do CEATEC; Local: PUC Campinas; Brazil, 2004.11.8.19. "Protein Dossier and STING Report: the database and user interface of the physical- chemical parameters describing the protein structure, function an binding".INRIA/CNRS Nancy, France; 2004

 

   2005

11.9.1. "Ferramentas da Bioinformática Estrutural". Centro Nacional de Pesquisa Tecnológica em Informáticapara a Agricultura - CNPTIA. Campinas, Brazil.11.9.2. "Proteoma e Recursos da Bioinformática". Centro Nacional de Pesquisa Tecnológica em Informáticapara a Agricultura - CNPTIA. Campinas, Brazil. April.11.9.3. "O que os 306 descritores de estrutura e função do STING_DB poderiam ensinar sobre a relação entre a sequência/estrutura/função das  proteínas". Doutorado Bioinformática Universidade Federal de Minas Gerais. Belo Horizonte, Brazil. June.11.9.4. "ISMB 2006 to be held in Fortaleza, Ceara, Brazil". ISMB 2005. Detroit, USA. June.11.9.5. "STING - A Web Server for Comprehensive Analysis of Protein Structure and Sequence". ISMB 2005. Detroit, USA. June.11.9.6. "The Identification of the Folding Essential Residues and Active Site Residues by looking at an extensive DB of the Structure Descriptors            in Diamond STING". Beckman Institute, University of Illinois. Urbana-Champaign, USA. July.11.9.7. "The identification of the folding essential residues and active site residues by looking at an extensive DB of the structure descriptors in Diamond STING". Department of Biochemistry and Molecular Biophysics, Columbia University, USA. July.11.9.8. "The Identification of the Folding Essential Residues and Active Site Residues by looking at an extensive DB of the Structure Descriptors in Diamond STING".Beckman Institute for Advanced Science and Technology. USA. June.11.9.9. "Como a bioinformática pode impulsionar o campo de saúde". Instituto de Pesquisa e Desenvolvimento da UNIVAP. São José dos Campos, Brazil. September.11.9.10. "How high performance computing can drive agriculture and health realted research". II

Fórum de Tecnologia e Aplicações de Sistemas  de Alto Desempenho. Rio de Janeiro, Brazil. October.11.9.11. "Diamond STING". NANOGEN - II Workshop de Nanotecnologia Aplicada às Ciências Biológicas e Genética. Universidade Estadual do Ceará. December.

 

   2006

11.10.1."Bioinformatics (Computational Biology) at Embrapa: 1989-2006 and beyond". Centro Nacional de Pesquisa Tecnológica em Informáticapara a Agricultura - CNPTIA. Campinas, Brazil.           11.10.2. "Studying the amino acid co-evolution in terms of protein stability and functionality".

Segundas Jornadas Iberoamericanas de Bioinformatica,Buenos Aires, December, 2-5 ,

Buenos Aires, Argentina.

   2007

         11.11.1. "Computational Biology and Bioinformatics". 6. Congresso Brasileiro de Agroinformática

- SBIAgro 2007 São Paulo, Brazil.          11.11.2. "Protein Folding Seen Through the Secondary Structure Element Dossier and Chameleon Sequences". 2d Latin American Protein Society Meeting (2LAPSM), Acapulco, Mexico.

2008    

         11.12.1. "The architecture of Proteins, nano and macro Engines and of the Software". - Regional Architect Forum 2008, Microsoft Brazil, São Paulo, Brazil.

11.12.2.“The Table of Interface Forming Residues as the Specificity Indicator for Serine Proteases Bound to Different Inhibitors “ BIOCOMP 2008, Las Vegas, NE, (July 2008) USA 

11.12.3. “Dossier of Secondary Structure Elemnts Amino Acid Properties “ISMB 2008, toronto, (July, 2008) Canda

11.12.4. “Contact coordination patterns and electrostatic potential at alpha carbon atoms: a dossier of pro-tein secondary structure elements“ Embnet 2008, Bari,(Sptember, 2008) Italia 

11.12.5. ““Embnet activities at the Campinas Node, SP – Brazil“ Embnet 2008, Bari,(Sptember, 2008) Italia

11.12.6“Structure Descriptors of Chameleon Sequences “ RIB 2008, Santiago de Chile (October 2008), Chile

11.12.7 “How did the structure function descriptors of proteins change with introduction of “remediated” pdb files - large scale db maintanance“ RIB 2008, Santiago de Chile (October 2008), Chile

 12. COURSES

This Section Updated: JANUARY 14, 2009

12.1."Drug design and structural Bioinformatics", 29 January - 08 February / 04 March - 08 March 2002, Centro Nacional de Pesquisa Tecnológica em Informática para a Agropecuária CNPTIA, Campinas, SP, Brazil.

12.2."Fisrt Sting Millennium Suite (SMS): tools to Analyze Macromolecular Structures and Applications in Chemogenomics", 29 - 30 October 2002, Centro Nacional de Pesquisa Tecnológica em Informática para a

Agropecuária CNPTIA, Campinas, SP, Brazil.

12.3."Bioinformática Estrutural", 07 - 17 April 2003, Centro Nacional de Pesquisa Tecnológica em Informática para a Agropecuária CNPTIA, Campinas, SP, Brazil.

12.4."Pan American Advanced Studies Institute - Knowledge Discovery in Genomic Databases"; 07 - 17 February 2004, Biotec Plaza Zona America;Montevideo Uruguay. 

12.5."WORKSHOP INTERNACIONAL DE NANOTECNOLOGIA APLICADA ÀS CIÊNCIAS BIOLÓGICAS E GENÉTICA" June 2004, FVA/CNPq; Fortaleza -Ceara, Brazil.

12.6."BIOINFORMÁTICA APLICADA À PROTEÔMICA".Septemeber - 2004, LNCC - Petropolis - Brazil. 

12.7. "Algorithms and Computational Methods for Biochemical and Evolutionary Networks (CompBioNets'04)". December - 2004. Universidade de Pernanbuco, Recife - Brazil; 

12.8."Diamond STING: suite of software for comprehensive protein structure/stability/function analysis" {80 hours} March 2005, La PLata - Argentina.

12.9."Bioinformática Estrutural - NG250A", August/September 2005, Centro Nacional de Pesquisa Tecnológica em Informática para a Agropecuária CNPTIA, Campinas, SP, Brazil. 

12.10. "Structural Bioinformatics" - {80 hours} September 2006, Embrapa Informatica Agropecuaria, Embrapa Bioinformatics Network, Campinas, SP, Brazil.

12.11. "Structural Computational Biology - using STING_DB to study protein structures " - {80 hours} February 2008, Embrapa Informatica Agropecuaria, Campinas, SP, Brazil.

12.12. "Structural Bioinformatics" - {120 hours} October/November 2008, Embrapa Informatica Agropecuaria and UNICAMP, Campinas, SP, Brazil.

13. PROJECTSThis Section Updated: January, 2009

Year Supporting Agency US$ R$ Project title

1 1990 IICA 120.000,00 Computer Modelling and visualisation

2 1994 FAPDF 210.000,00 Bioinformatics in service of molecular biology and biotechnology

3 1994 SGI 30.000,00 Computational Structural Biology in service of agro-business

4 1997/8 NSF 50.000,00 Sequente To and withIN Graphics - STING

5 198/9 FAPDF 100.000,00 Computer visualisation of quarantene pests

6 2001 FAPSP 285.741,10 185.731,72 Structural BioInformatics Research and Service Center (CBI)

7 2001 CNPq 240.000,00Bioinformatics: From Gene Annotation to Development of

Drugs - Implementation of new Computational Tools, Proprietary Data Banks and Metacomputing Concept

8 2002 FINEP 381.444,16 Structural Bioinformatics Applications with high demand for available CPU time in post-genomic era

9 2002 CNPq 55.581,26 Expanding STING_DB

10 2004 SUN Computers 150.000,00 STING_RDB

11 2006 FAPSP 80.000,00 ISMB 2006 and X-meeting 2006 support

12 2007 SUN Computers 150.000,00 GenoProt PLUS - pipline for deciphering function of

proteins identified by Brazilian genomes projects

13 2007 Embrapa- MP1 - (2.300.000,00) Co-participation: Functional Foods and Nutrigenomics -

Computational Biology - structure analysis

14 2008 CNPq (55.000,00) Co-participation: Nanotecnology Impacts

15 2008 CENAPAD - - STING_DB update

16 2008 FAPBA     Catalisadores e processos enzimáticos para produção de biodiesel

Total 885.741,10 1.152.757,14

Per Year 17 years total 52.102,42 67.809,24

Values are cited for the date received (consequently should be indexed for both currency fluctuations)

14. PROFESSIONAL REFERENCES

14.1. Antony Crofts, Professor and Head, Dept. of Physiology and Biophysics, University of Illinois at Urbana-Champaign 524 Burrill Hall, 407 S. Goodwin Avenue, Urbana, Il, 61801 USAphone: (217) 333-2043e-mail:Crofts@pop.life.uiuc.eduor: a-crofts@uiuc.eduhttp://www.life.uiuc.edu/~crofts

14.2. Colin Wraight, Associate Professor, Dept. of Physiology and Biophysics, University of Illinois at Urbana-Champaign 524 Burrill Hall, 407 S. Goodwin Avenue, Urbana, Il, 61801USAphone: (217) 333-3245e-mail: cwraight@pop.life.uiuc.edu

14.3.Eduardo Tadao Takahashi, Coordenador - Geral Adjunto, Rede Nacional de Pesquisa, CNPq/SCT - PR, Rua Dr. Antonio Augusto de Almeida, 334, Cidade Universitária, CEP 13083 CAMPINAS/SP - Brazil.phone: +55 192 39.4141fax: +55 192 39.3070e-Mail: tadao@na-cp.rnp.br

14.4. Barry Honig, Professor, Dept of Biochemistry & Molecular Biophysics - Columbia University, New York , USAphone: (212) 305-7970 fax: (212) 305-6926 e-Mail: honig@bass.bioc.columbia.edu or: bh6@columbia.edu