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Brownian Dynamics Simulation of Peptides with the University of Houston Brownian Dynamics (UHBD) Program

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Part of the Methods in Molecular Biology book series (MIMB, volume 1268)

Abstract

This chapter provides the background theory and a practical protocol for performing Brownian dynamics simulation of peptides. Brownian dynamics simulation represents a complementary approach to Monte Carlo and molecular dynamics methods. Unlike Monte Carlo methods, it could provide dynamical information in a timescale longer than the momentum relaxation time. On the other hand, it is faster than molecular dynamics by approximating the solvent by a continuum and by operating in the over-damped limit. This chapter introduces the use of the University of Houston Brownian Dynamics (UHBD) program [1, 2] to perform Brownian dynamics simulation on peptides.

Key words

Brownian dynamics simulation UHBD program Helix-capping motifs Conformational distribution of peptides 
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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  1. 1.Department of Biochemistry, Cellular & Molecular BiologyUniversity of TennesseeKnoxvilleUSA
  2. 2.Department of Chemistry and BiochemistryUniversity of Missouri St LouisSt LouisUSA

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