Relaxation of backbone bond geometry improves protein energy landscape modeling.

ABSTRACT: A key issue in macromolecular structure modeling is the granularity of the molecular representation. A fine-grained representation can approximate the actual structure more accurately, but may require many more degrees of freedom than a coarse-grained representation and hence make conformational search more challenging. We investigate this tradeoff between the accuracy and the size of protein conformational search space for two frequently used representations: one with fixed bond angles and lengths and one that has full flexibility. We performed large-scale explorations of the energy landscapes of 82 protein domains under each model, and find that the introduction of bond angle flexibility significantly increases the average energy gap between native and non-native structures. We also find

SUBMITTER: Conway P 

PROVIDER: S-EPMC3892298 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature