Equilibrium sampling of polypeptides using a polymer-growth strategy

PHYS 357

Artem B. Mamonov, artem@pitt.edu, Department of Computational Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Ave, BST3 Rm 3088, Pittsburgh, PA 15213 and Daniel M. Zuckerman, dmz@ccbb.pitt.edu, Department of Computational Biology, University of Pittsburgh, 3051 Fifth Ave, Pittsburgh, PA 15260.
Conventional methods for high quality sampling of proteins such as molecular dynamics (MD) are expensive because they generate structurally correlated configurations and therefore move slowly in configuration space. We adapted a polymer sampling approach to generate configurations with much smaller correlations. The two main components of the new procedure are the combination of fragments to grow a polypeptide chain and re-weighting to conform to a Boltzmann factor distribution. This procedure was applied to generate equilibrium ensembles of several polypeptides. We performed a statistical efficiency comparison with long time Langevin dynamics trajectories.
 

PHYS Poster Session - Multiscale Modeling in Biophysics
7:30 PM-10:00 PM, Wednesday, April 9, 2008 Morial Convention Center -- Hall A, Poster

Sci-Mix
8:00 PM-10:00 PM, Monday, April 7, 2008 Morial Convention Center -- Hall A, Sci-Mix

Division of Physical Chemistry

The 235th ACS National Meeting, New Orleans, LA, April 6-10, 2008