Protein Structure Comparison and Motif Discovery


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Table of Contents

Protein Structure Comparison and Motif Discovery


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

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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

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Structure Description - Levels

Structure Description - Features

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Equivalences and Alignments

Scoring Equivalences

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Comparison Algorithms

Dynamic Programming - DP

Examples of DP based methods

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Multiple Structure Comparison


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

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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



Author: Inge Jonassen


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