Protein structure classification

16
Protein Classification And Structure prediction

TAGS:

Transcript of Protein structure classification

Page 1: Protein structure classification

Protein ClassificationAnd Structureprediction

Page 2: Protein structure classification

Ramachandran plot

Page 3: Protein structure classification

Turns and Loops

Page 4: Protein structure classification

Tertiary structureMotifs: -Also called supersecondary structures or folds-Stable arrangements of several elements of secondary structure and connections between them

Domains: Polypeptides with more than a few hundred amino acid residues often fold into two or more stable, globular units

Page 5: Protein structure classification

Stable folding patterns in proteins

Page 6: Protein structure classification

Stable folding patterns in proteins

Page 7: Protein structure classification

Stable folding patterns in proteins

Page 8: Protein structure classification

Stable folding patterns in proteins

Page 9: Protein structure classification

Quaternary structureThe spatial arrangement of different subunits

Forces involved are,1. Vander Waals2. London Dispersions3. Salt bridges4. H-bonds

Page 10: Protein structure classification

Protein structure classification1. Alpha or α/α 2. Beta or β /β3. Alpha/Beta or α/β 4. Alpha and Beta or α+β

Page 11: Protein structure classification

Steric properties of amino acids can greatly affect the localstructures that a protein adopts

Structural configuration Amino acidPropensity for alpha-helix Ala, Leu, GluDisrupt alpha-helix Ser, Asp, AsnPropensity for Beta-sheets and disrupt alpha-helix Val and IlePropensity for turns Gly, Pro, Asp

Page 12: Protein structure classification

Protein structure DatabasesProtein Data BankLarge global repository for the processing and distribution of 3-D macromolecular structure data (experimental)

MMDB (Molecular modelling Database)Macromolecular 3D structures as well as tools for theirvisualization and comparative analysis

Page 13: Protein structure classification

Protein structure Visualization Databases and tools

Cn3-DStructure and sequence alignment viewer for NCBI databases

RasMolOne of the most popular tools for protein structure visualization

Swiss-PDB Viewer An interface to analyze several proteins at the same timeIt is tightly linked to Swiss-model, an automated homologymodelling server

Page 14: Protein structure classification

Protein structure Visualization Databases and tools

KinemageAn illustration presented as an interactive computer display

PDBsumPictorial summary of the key information on each macromolecular structure from PDB

Page 15: Protein structure classification

Protein structure alignment

VAST (Vector alignment Search Tool)Developed at NCBIUsed to identify similar protein 3D structures in MMDB/PDB

DALI ServerAn automated protein structure alignment tool

Page 16: Protein structure classification

Domain Architecture Databases

CDD (Conserved Domain Database)NCBI databaseCollection of sequence alignments and profiles, representing protein


CLASSIFICATION OF PROTEIN STRUCTUREShome.ku.edu.tr/~okeskin/CMSE520/lecture7.pdf · 1 CLASSIFICATION OF PROTEIN STRUCTURES Comparing Protein Structures: Why? • detect evolutionary

CLASSIFICATION OF PROTEIN STRUCTUREShome.ku.edu.tr/~okeskin/CMSE520/lecture7.pdf · 1 CLASSIFICATION OF PROTEIN STRUCTURES Comparing Protein Structures: Why? • detect evolutionary

Chap. 4B The Three-dimensional Structure of Proteins Topics Overview of Protein Structure Protein Secondary Structure Protein Tertiary and Quaternary Structure.

Chap. 4B The Three-dimensional Structure of Proteins Topics Overview of Protein Structure Protein Secondary Structure Protein Tertiary and Quaternary Structure.

Protein structures. Protein Structure Why protein structure? The basics of protein Basic measurements for protein structure Levels of protein structure.

Protein structures. Protein Structure Why protein structure? The basics of protein Basic measurements for protein structure Levels of protein structure.

BMMB597E Protein Evolution Protein classification 1.

BMMB597E Protein Evolution Protein classification 1.

Protein Tertiary Structure Prediction. Protein Structure Prediction & Alignment Protein structure Secondary structure Tertiary structure Structure prediction.

Protein Tertiary Structure Prediction. Protein Structure Prediction & Alignment Protein structure Secondary structure Tertiary structure Structure prediction.

Microsoft Word - Protein Structure Worksheet.rtfsciencestephenson.com › wp...Protein-Structure.docx  · Web viewUnderstanding Protein Structure. Part 1: Primary Protein Structure.

Microsoft Word - Protein Structure Worksheet.rtfsciencestephenson.com › wp...Protein-Structure.docx  · Web viewUnderstanding Protein Structure. Part 1: Primary Protein Structure.

PROTEIN STRUCTURE CLASSIFICATION SUMI SINGH (sxs5729)

PROTEIN STRUCTURE CLASSIFICATION SUMI SINGH (sxs5729)

Protein Structure Classification - Computer Science- …nook.cs.ucdavis.edu/~koehl/Teaching/ECS129/Reprints/ProtStruct...1 Protein Structure Classification Patrice Koehl, Department

Protein Structure Classification - Computer Science- …nook.cs.ucdavis.edu/~koehl/Teaching/ECS129/Reprints/ProtStruct...1 Protein Structure Classification Patrice Koehl, Department

Protein Structure Prediction Dr. G.P.S. Raghava Protein Sequence + Structure.

Protein Structure Prediction Dr. G.P.S. Raghava Protein Sequence + Structure.

Automatic Classification of Protein Structure Using the ...

Automatic Classification of Protein Structure Using the ...

Protein Structure...Protein Structure Analysis The complexities of protein structure make the elucidation of a complete protein structure extremely dificult even with the most advanced

Protein Structure...Protein Structure Analysis The complexities of protein structure make the elucidation of a complete protein structure extremely dificult even with the most advanced

V. Evolution of Protein Structure and Function Protein structure classification Structural relationships among homologous proteins Changes in proteins.

V. Evolution of Protein Structure and Function Protein structure classification Structural relationships among homologous proteins Changes in proteins.

SESSION PROTEIN CLASSIFICATION, STRUCTURE …...Figure 1: Steps in the protein structure-function analysis. Figure 2: Feature vector construction, unfolded 3D-coordinates. represents

SESSION PROTEIN CLASSIFICATION, STRUCTURE …...Figure 1: Steps in the protein structure-function analysis. Figure 2: Feature vector construction, unfolded 3D-coordinates. represents

Protein Structure - DSpace@MIT Home · Introduction to Protein Structure & Classification Protein structures basics where to find them how to look at them what they can tell you structural

Protein Structure - DSpace@MIT Home · Introduction to Protein Structure & Classification Protein structures basics where to find them how to look at them what they can tell you structural

Protein Structure Analysis & Protein-Protein Interactions · Protein Structure Analysis & Protein-Protein Interactions David Wishart ... Protein Data Bank ... •Objective is to match

Protein Structure Analysis & Protein-Protein Interactions · Protein Structure Analysis & Protein-Protein Interactions David Wishart ... Protein Data Bank ... •Objective is to match

1 Protein Structure, Structure Classification and Prediction Bioinformatics X3 January 2005 P. Johansson, D. Madsen Dept.of Cell & Molecular Biology, Uppsala.

1 Protein Structure, Structure Classification and Prediction Bioinformatics X3 January 2005 P. Johansson, D. Madsen Dept.of Cell & Molecular Biology, Uppsala.

Protein Structure: protein folding

Protein Structure: protein folding

CMB20190416 protein structure predictionliacs.leidenuniv.nl › ... › CMB20190416_protein_structure_prediction.pdf · Protein secondary structure prediction • Protein secondary

CMB20190416 protein structure predictionliacs.leidenuniv.nl › ... › CMB20190416_protein_structure_prediction.pdf · Protein secondary structure prediction • Protein secondary

PDB-Protein Data Bank SCOP –Protein structure classification CATH –Protein structure classification genTHREADER–3D structure prediction Swiss-Model–3D.

PDB-Protein Data Bank SCOP –Protein structure classification CATH –Protein structure classification genTHREADER–3D structure prediction Swiss-Model–3D.

Chap. 4A The Three-dimensional Structure of Proteins Topics Overview of Protein Structure Protein Secondary Structure Protein Tertiary and Quaternary Structure.

Chap. 4A The Three-dimensional Structure of Proteins Topics Overview of Protein Structure Protein Secondary Structure Protein Tertiary and Quaternary Structure.