Fast protein loop sampling and structure prediction using distance-guided sequential chain-growth Monte Carlo method.

ABSTRACT: Loops in proteins are flexible regions connecting regular secondary structures. They are often involved in protein functions through interacting with other molecules. The irregularity and flexibility of loops make their structures difficult to determine experimentally and challenging to model computationally. Conformation sampling and energy evaluation are the two key components in loop modeling. We have developed a new method for loop conformation sampling and prediction based on a chain growth sequential Monte Carlo sampling strategy, called Distance-guided Sequential chain-Growth Monte Carlo (DISGRO). With an energy function designed specifically for loops, our method can efficiently generate high quality loop conformations with low energy that are enriched with near-native loop structu

SUBMITTER: Tang K 

PROVIDER: S-EPMC3998890 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature