Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol

Details Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol

2004-12-17

arxiv.org/abs/physics/0412116v1

Physics

Biological Physics

24 pages, 4 figures, 2 tables

Scientific paper

We study the conformational equilibria of two peptides using a novel statistical mechanics approach designed for calculating free energy differences between highly dis-similar conformational states. Our results elucidate the contrasting roles of entropy in implicitly solvated leucine dipeptide and decaglycine. The method extends earlier work by Voter, and overcomes the notorious "overlap" problem in free energy computations by constructing a mathematically equivalent calculation with high conformational similarity. The approach requires only equilibrium simulations of the two states of interest, without the need for sampling transition states. We discuss extensions of the approach to binding affinity estimation and explicitly solvated systems, as well as possible optimizations.

Affiliated with

Also associated with

No associations

Rating

Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-332714