An estimate of the numbers and density of low-energy structures (or decoys) in the conformational landscape of proteins.

ABSTRACT:

Background

The conformational energy landscape of a protein, as calculated by known potential energy functions, has several minima, and one of these corresponds to its native structure. It is however difficult to comprehensively estimate the actual numbers of low energy structures (or decoys), the relationships between them, and how the numbers scale with the size of the protein.

Methodology

We have developed an algorithm to rapidly and efficiently identify the low energy conformers of oligo peptides by using mutually orthogonal Latin squares to sample the potential energy hyper surface. Using this algorithm, and the ECEPP/3 potential function, we have made an exhaustive enumeration of the low-energy structures of peptides of different lengths, and have extrapolated these re

SUBMITTER: Vadivel K 

PROVIDER: S-EPMC2663821 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature