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DNA/protein modeling

Part 4. Bioinformatics

4.6. Methods for Structure Analysis and Prediction

Short Specialist Review

  1. Richard Lavery

Published Online: 15 JAN 2005

DOI: 10.1002/047001153X.g406317

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Lavery, R. 2005. DNA/protein modeling. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.6:77.

Author Information

  1. Institut de Biologie Physico-Chimique, Paris, France

Publication History

  1. Published Online: 15 JAN 2005

Abstract

Considerable progress has been made in modeling both DNA and protein-DNA complexes. The results help explain how specific base sequences can modify the properties of the double helix, influencing its structure and mechanical properties. These changes are important for the understanding of DNA recognition and packing. In the case of protein-DNA complexes, modeling can help in identifying protein-binding sites and in understanding the consequences of mutations in either of the interacting partners. Modeling can also be used to obtain structural and dynamic information from a variety of experimental data and will also contribute to extending the nanotechnological applications of the double helix.

Keywords:

  • DNA;
  • protein-DNA;
  • molecular modeling;
  • molecular dynamics;
  • DNA curvature;
  • DNA packing;
  • elastic rod;
  • binding specificity;
  • weight matrix