Chapter 7. Prediction of Molecular Interactions from 3D-Structures: From Small Ligands to Large Protein Complexes

  1. Janusz M. Bujnicki4,5
  1. Kengo Kinoshita1,
  2. Hidetoshi Kono2 and
  3. Kei Yura3

Published Online: 18 DEC 2008

DOI: 10.1002/9780470741894.ch7

Prediction of Protein Structures, Functions, and Interactions

Prediction of Protein Structures, Functions, and Interactions

How to Cite

Kinoshita, K., Kono, H. and Yura, K. (2008) Prediction of Molecular Interactions from 3D-Structures: From Small Ligands to Large Protein Complexes, in Prediction of Protein Structures, Functions, and Interactions (ed J. M. Bujnicki), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470741894.ch7

Editor Information

  1. 4

    Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland

  2. 5

    Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland

Author Information

  1. 1

    Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan

  2. 2

    Computational Biology, Quantum Beam Science Directorate, Japan Atomic Energy Agency, 8-1 Umemidai, Kizugawa, Kyoto 619-0215, Japan

  3. 3

    Center for Informational Biology, Ochanomizu University, 2-1-1, Otsuka, Bunkyo, Tokyo 112-8610, Japan

Publication History

  1. Published Online: 18 DEC 2008
  2. Published Print: 19 DEC 2008

ISBN Information

Print ISBN: 9780470517673

Online ISBN: 9780470741894

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Keywords:

  • protein–ligand interactions;
  • 3D-structures and molecular interaction prediction;
  • protein–DNA interactions;
  • gene expression regulation;
  • prediction methods - sequence-based and structure-based;
  • naive Bayes classifier method in RNABindR;
  • homologous interactions;
  • protein-protein docking and ZDOCK algorithms

Summary

This chapter contains sections titled:

  • Introduction

  • Protein–Ligand Interactions

  • Protein–DNA Interactions

  • Protein–RNA Interactions

  • Protein–Protein Interactions

  • References