Chapter 5. Template-Free Predictions of Three-Dimensional Protein Structures: From First Principles to Knowledge-Based Potentials

  1. Janusz M. Bujnicki2,3
  1. Dominik Gront,
  2. Dorota Latek,
  3. Mateusz Kurcinski and
  4. Andrzej Kolinski

Published Online: 18 DEC 2008

DOI: 10.1002/9780470741894.ch5

Prediction of Protein Structures, Functions, and Interactions

Prediction of Protein Structures, Functions, and Interactions

How to Cite

Gront, D., Latek, D., Kurcinski, M. and Kolinski, A. (2008) Template-Free Predictions of Three-Dimensional Protein Structures: From First Principles to Knowledge-Based Potentials, in Prediction of Protein Structures, Functions, and Interactions (ed J. M. Bujnicki), John Wiley & Sons, Ltd, Chichester, UK. doi: 10.1002/9780470741894.ch5

Editor Information

  1. 2

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

  2. 3

    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. Faculty of Chemistry, University of Warsaw, Pateura 1, 02-093 Warsaw, Poland

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:

  • de novo protein modeling;
  • force fields and scoring functions;
  • quantum-mechanical computation;
  • protein molecule - choice of representation;
  • high resolution lattice models;
  • SICHO (SIde Chain Only) model;
  • residual dipolar couplings (RDC) and NOEs;
  • multiple sequence alignments and solvent accessibility;
  • de novo protein structure prediction

Summary

This chapter contains sections titled:

  • Introduction

  • Force Fields and Scoring Functions

  • Reduced Models: Representation and Conformational Sampling

  • Successful Approaches to de Novo Protein Modeling

  • Multiscale Modeling

  • Experimental and Predicted Restraints in Guided de Novo Modeling

  • Perspectives

  • References