Chapter I-6. Protein Structure Prediction

  1. Prof. Dr. Thomas Lengauer Ph.D.
  1. Prof. Dr. Ralf Zimmer1 and
  2. Prof. Dr. Thomas Lengauer Ph.D.3,†

Published Online: 1 APR 2004

DOI: 10.1002/3527601481.ch6

Bioinformatics - From Genomes to Drugs

Bioinformatics - From Genomes to Drugs

How to Cite

Zimmer, R. and Lengauer, T. (2001) Protein Structure Prediction, in Bioinformatics - From Genomes to Drugs (ed T. Lengauer), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, FRG. doi: 10.1002/3527601481.ch6

Editor Information

  1. Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany

Author Information

  1. 1

    Ludwig-Maximilians-Universität München, Institut für Informatik, Theresienstraße 39, 80333 München, Germany

  2. 3

    Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany

  1. Max-Planck-Institute for Computer Science, Stuhlsatzenhausweg 85, 66123 Saarbrücken, Germany

Publication History

  1. Published Online: 1 APR 2004
  2. Published Print: 1 NOV 2001

Book Series:

  1. Methods and Principles in Medicinal Chemistry

Book Series Editors:

  1. Prof. Dr. Raimund Mannhold4,
  2. Prof. Dr. Hugo Kubinyi5 and
  3. Prof. Dr. Gerd Folkers6

Series Editor Information

  1. 4

    Biomedical Research Center, Molecular Drug Research Group, Heinrich-Heine-Universität, Universitätsstraße 1, D-40225 Düsseldorf, Germany

  2. 5

    BASF AG, Ludwigshaften, c/o Donnersbergstrasse g, D-67256 Weisenheim am Sand, Germany

  3. 6

    Department of Applied Biosciences, ETH Zürich, Winterthurer Str. 190, CH-8057 Zürich, Switzerland

ISBN Information

Print ISBN: 9783527299881

Online ISBN: 9783527601486

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Keywords:

  • protein structure prediction;
  • structural genomics

Summary

This chapter contains sections titled:

  • Overview

    • Definition of terms

    • What is covered in this chapter

  • Data

    • Input data

    • Output data

    • Additional input data

    • Structure comparison and classification

    • Scoring functions and (empirical) energy potentials

  • Methods

    • Secondary structure prediction

    • Knowledge-based 3D structure prediction

  • Results

    • Remote homology detection

    • Structural genomics

    • Selecting targets for structural genomics

    • Genome annotation

    • Sequence-to-structure-to-function paradigm

  • Validation of predictions

    • Benchmark set tests

    • Blind prediction experiments (CASP)

  • Conclusion: strengths and limitations

    • Threading

    • Strengths

    • Limitations

  • Accessibility