Work

Targeted conformational search with map-restrained self-guided Langevin dynamics: Application to flexible fitting into electron microscopic density maps

Year: 2013

Type: article

Abstract: We present a map-restrained self-guided Langevin dynamics (MapSGLD) simulation method for efficient targeted conformational search. The targeted conformational search represents simulations under restraints defined by experimental observations and/or by user specified structural requirements. Through map-restraints, this method provides an efficient way to maintain substructures and to set structure targets during conformational searching. With an enhanced conformational searching ability of self-guided Langevin dynamics, this approach is suitable for simulating large-scale conformational changes, such as the formation of macromolecular assemblies and transitions between different conformational states. Using several examples, we illustrate the application of this method in flexible fitting of atomic structures into density maps derived from cryo-electron microscopy.

Source: Journal of Structural Biology

DOI: 10.1016/j.jsb.2013.07.006

Authors: Xiongwu Wu, Sriram Subramaniam, David A. Case, Katherine W. Wu, Bernard R. Brooks

Institutions: National Institutes of Health, National Heart, Lung, and Blood Institute, National Cancer Institute, Rutgers, The State University of New Jersey

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $4,350

Funders: National Institutes of Health, National Heart, Lung, and Blood Institute, National Cancer Institute