Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps.

ABSTRACT: Flexible fitting computational algorithms are often useful to interpret low-resolution maps of many macromolecular complexes generated by electron microscopy (EM) imaging. One such atomistic simulation technique is molecular dynamics flexible fitting (MDFF), which has been widely applied to generate structural models of large ribonucleoprotein assemblies such as the ribosome. We have previously shown that MDFF simulations of globular proteins are sensitive to the resolution of the target EM map and the strength of restraints used to preserve the secondary structure elements during fitting (Vashisth, H.; et al. Structure 2012, 20, 1453-1462). In this work, we aim to systematically examine the quality of structural models of various nucleic acids obtained via MDFF by varying the map resoluti

SUBMITTER: Vashisth H 

PROVIDER: S-EPMC3690198 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature