Efficient conformational space exploration in ab initio protein folding simulation.

ABSTRACT: Ab initio protein folding simulation largely depends on knowledge-based energy functions that are derived from known protein structures using statistical methods. These knowledge-based energy functions provide us with a good approximation of real protein energetics. However, these energy functions are not very informative for search algorithms and fail to distinguish the types of amino acid interactions that contribute largely to the energy function from those that do not. As a result, search algorithms frequently get trapped into the local minima. On the other hand, the hydrophobic-polar (HP) model considers hydrophobic interactions only. The simplified nature of HP energy function makes it limited only to a low-resolution model. In this paper, we present a strategy to derive a non-unifor

SUBMITTER: Ullah A 

PROVIDER: S-EPMC4555859 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature