Proteomics and Protein Structure Introduction to Bioinformatics - - PowerPoint PPT Presentation

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Proteomics and Protein Structure Introduction to Bioinformatics - - PowerPoint PPT Presentation

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Proteomics and Protein Structure Introduction to Bioinformatics Dortmund, 16.-20.07.2007 Lectures: Sven Rahmann Exercises: Udo Feldkamp, Michael Wurst 1 Overview Proteomics tools for almost all purposes ExPASy Server (Expert Protein

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Proteomics and Protein Structure

Introduction to Bioinformatics Dortmund, 16.-20.07.2007 Lectures: Sven Rahmann Exercises: Udo Feldkamp, Michael Wurst

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Overview

  • Proteomics tools for almost all purposes

– ExPASy Server (Expert Protein Annotation System)

  • Structural Classification of Proteins

– CATH and SCOP databases

  • 3D protein structure information and visualization

– wwPDB containing RCSB-PDB – different embedded visualization tools

  • Specialized protein databases (e.g., GPCR DB)
  • CASP: protein structure predition contest
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ExPASy: Expert Protein Analysis SYstem

  • URL: http://expasy.org/

Access proteomics tools Search one of the databases

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ENZYME Database

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Hundreds of Proteomics Tools

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Protein Domains

  • “building blocks” of proteins
  • functional units
  • Major Domain Databases:

– Pfam – SMART

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Structural Classification: CATH

  • http://www.cathdb.info/latest/index.html
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Structural Classification: SCOP

  • http://scop.mrc-lmb.cam.ac.uk/scop/
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SCOP

  • 4 Levels

– Class (alpha; beta; alpha/beta; alpha+beta) – Fold (1000 folds) – superfamily (evolutionary relationship) – family

  • Proteins in each family consist of the same

domains

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wwPDB / RCSB-PDB

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Viewing PDB information

Start 3D structure viewers here

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Specialized Protein DBs

  • http://www.gpcr.org/
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CASP: Biannual structure prediction contest

  • Critical Assesment of (Protein) Structure

Prediction: http://predictioncenter.org/

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Homology Search

  • Structure Predication by Homology search:

– find structure in PDB with similar sequence as

query protein

  • High sequence similarity implies evolutionary

relation and structural similarity

  • However: structural similarity does not imply

high sequence similarity (even 20% is ok)

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Threading

  • Try to fit a given sequence on all known

structures

  • Background: Angles of bonds between different

amino acids must be in a limited range

  • “dual” to Homology modeling
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Ab Initio Prediction

  • Molecular Dynamics (“low level”)

– propose a confirmation, compute its stability, modify – very compute-intensive – only for short peptides

  • Fragment Assembly

– Assemble predicted 3D-structures of short

fragments into a larger 3D structure