20. Modeling Mutations in Proteins Using Medusa and Discrete Molecule Dynamics

  1. Huzefa Rangwala2 and
  2. George Karypis3
  1. Shuangye Yin,
  2. Feng Ding and
  3. Nikolay V. Dokholyan

Published Online: 7 SEP 2010

DOI: 10.1002/9780470882207.ch20

Introduction to Protein Structure Prediction: Methods and Algorithms

Introduction to Protein Structure Prediction: Methods and Algorithms

How to Cite

Yin, S., Ding, F. and Dokholyan, N. V. (2010) Modeling Mutations in Proteins Using Medusa and Discrete Molecule Dynamics, in Introduction to Protein Structure Prediction: Methods and Algorithms (eds H. Rangwala and G. Karypis), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470882207.ch20

Editor Information

  1. 2

    Department of Computer Science, George Mason University, Fairfax, VA 22030, USA

  2. 3

    Department of Computer Science, University of Minnesota Minneapolis, MN 55455, USA

Author Information

  1. Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA

Publication History

  1. Published Online: 7 SEP 2010
  2. Published Print: 12 NOV 2010

Book Series:

  1. Wiley Series on Bioinformatics: Computational Techniques and Engineering

Book Series Editors:

  1. Yi Pan and
  2. Albert Zomaya

ISBN Information

Print ISBN: 9780470470596

Online ISBN: 9780470882207

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Keywords:

  • modeling mutations in proteins - using Medusa and discrete molecule dynamics;
  • Medusa protein design suite, modeling substitution mutations - side chain conformations efficiently sampled by Monte Carlo (MC) simulations, using backbone-dependent rotamers;
  • modeling series of T4 lysozyme mutations - Medusa and DMD methods, prediction errors existing in mutants

Summary

This chapter contains sections titled:

  • Introduction

  • Methods

  • Results and Discussion

  • Conclusion and Future Directions

  • Acknowledgments

  • References