Table of Contents
Protein Structure Comparison and Motif Discovery
Outline
Families, patterns, motifs
Example sequence pattern (zinc finger c2h2)
Prosite: Patterns for classification
Motif Usage
Protein Sequence Motif Databases
InterPro - EU funded collaboration between the databases
Motifs in Protein Analysis
Protein Structure Motif Databases
Structure Classification
Strategy for developing motifs
PPT Slide
PPT Slide
A Three Steps Approach to Pattern Discovery
Algorithmic Approaches to Pattern Discovery
Pattern Driven - pruning the search space
Some sequence driven algorithms:
Some pattern driven algorithms:
An Example Algorithm: Pratt
Pratt - functionality
Pratt - Example
Structure Comparison
PPT Slide
PPT Slide
Structure Description - Levels
Structure Description - Features
PPT Slide
Equivalences and Alignments
Scoring Equivalences
PPT Slide
Comparison Algorithms
Dynamic Programming - DP
Examples of DP based methods
PPT Slide
Multiple Structure Comparison
Framework
SPratt - Pattern Driven Algorithm for the Discovery of Structure Motifs
SPratt - Idea
Structure - represent each residue’s neighbourhood
Mark all residues within d Angstrom
Make neighbour string - C-terminal direction
Make neighbour string - N-terminal direction
SPratt - Neighbour Strings
SPratt - Discovery Algorithm
SPratt ranking of patterns
Example output: Cystein proteases
RMSd matrix
SPratt: Structures ? Motif
Combining SPratt with SAP
PPT Slide
SAP output - cystein proteases
SAP output - 2Fe2S Ferrodoxins
Test Cases - Summary of SPratt runs
Future/ongoing work: Combining SPratt with MulSAP
Work in progress - SPratt2
Performance on test cases used for SPratt
Mining PDB with SPratt2
New problems for mining approach
Possible Extensions of the Algorithms
Summary
Acknowledgments
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