Protein Structure Analysis Online

Maria A. Miteva1, Emil Alexov2, Bruno O. Villoutreix1

1 Inserm U648, University of Paris, Paris, France, 2 Clemson University, South Carolina
Publication Name:  Current Protocols in Protein Science
Unit Number:  Unit 2.13
DOI:  10.1002/0471140864.ps0213s50
Online Posting Date:  November, 2007
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Computational biology/chemistry tools are used in most areas of life/health science research. These methods are continually being developed and their use can present difficulties for both experienced and novice investigators. To facilitate the use of these applications, many packages have been implemented online during these last 5 years. This unit focuses on online computational methods with a special emphasis on structural refinement/atomic simulations, protein electrostatic calculations, searches for functional sites, searches for druggable pockets, protein docking and small molecule docking, and prediction of potential impact of amino acid variations on the structure and function of the protein molecules. Curr. Protoc. Protein Sci. 50:2.13.1‐2.13.23. © 2007 by John Wiley & Sons, Inc.

Keywords: structural bioinformatics; electrostatics; simulations; docking; on‐line tools; druggable pocket

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Table of Contents

  • Introduction
  • Visualization, Structural Refinement, Simulations
  • Electrostatics
  • Finding Hot Spots and Functional Sites
  • Prediction of Druggable Pocket
  • Protein‐Protein and Protein–Small Molecule Interactions
  • Analysis of Point Mutations
  • Conclusion
  • Acknowledgments
  • Literature Cited
  • Figures
  • Tables
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Literature Cited

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