Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University...

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Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005

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Transcript of Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University...

Page 1: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Sequence/Structure Alignment Resources from NCBI

Steve Bryant

Protein Data BankRutgers University

November 19, 2005

Page 2: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

… Structure look-up tools

… Structure-structure alignments

… Alignment tools in client software

… Conserved domain family alignments *

… Domain subfamily analysis tools *

Sequence / Structure Alignment Resources from NCBI…

Page 3: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Entrez Search Engine ...

Page 4: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Entrez Retrieval System ...

Protein Sequences

MEDLINEAbstracts

BLASTSequenceSimilarity

Protein Sequences

3D Structures

Nucleotide Sequences

Term FrequencyStatistics

VAST StructureSimilarity

BLASTSequenceSimilarity

1,500,000 users ...60,000,000 hits ...

… per day

Page 5: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Entrez Search Engine ...

Page 6: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Protein Sequence Records ...

Page 7: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

PubMed Links ...

Page 8: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

PubMed Links ...

Page 9: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Related Structure Links ...

Page 10: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Related Structure Links ...

Page 11: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Related Structure Link ...

Page 12: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Related Structure Alignment ...

Page 13: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Related Structure Alignment …

Cn3D

C:\Users\bryant\cdd\cn3d.exe c:\users\bryant\d\demo\2a14.val
Page 14: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Related Structure Links ...

Page 15: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Related Structure Link ...

Page 16: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Structure Neighbors of 2A14 ...

Page 17: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Structure Neighbor Alignment …

Cn3D

C:\Users\bryant\cdd\cn3d.exe c:\users\bryant\d\demo\2a141hnn.val
Page 18: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Align Target to Template …

Cn3D

C:\Users\bryant\cdd\cn3d.exe c:\users\bryant\d\demo\2a141hnn1.val
Page 19: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Target-Template Alignment …

C:\Users\bryant\cdd\cn3d.exe c:\users\bryant\d\demo\2a141hnn2.val
Page 20: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Leptin Threading Prediction, 1995 …

Page 21: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

Threading Leptin 2005 …

Cn3D

C:\Program Files\NCBI\Cn3D 4.1\cn3d.exe c:\users\bryant\d\demo\1irl1ax8.val
Page 22: Sequence/Structure Alignment Resources from NCBI Steve Bryant Protein Data Bank Rutgers University November 19, 2005.

… Structure look-up tools

… Structure-structure alignments

… Alignment tools in client software

… Conserved domain family alignments *

… Domain subfamily analysis tools *

Sequence / Structure Alignment Resources from NCBI…


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