Toward a detailed understanding of search trajectories in fragment assembly approaches to protein structure prediction.

ABSTRACT: Energy functions, fragment libraries, and search methods constitute three key components of fragment-assembly methods for protein structure prediction, which are all crucial for their ability to generate high-accuracy predictions. All of these components are tightly coupled; efficient searching becomes more important as the quality of fragment libraries decreases. Given these relationships, there is currently a poor understanding of the strengths and weaknesses of the sampling approaches currently used in fragment-assembly techniques. Here, we determine how the performance of search techniques can be assessed in a meaningful manner, given the above problems. We describe a set of techniques that aim to reduce the impact of the energy function, and assess exploration in view of the search sp

SUBMITTER: Kandathil SM 

PROVIDER: S-EPMC4982100 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature