Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change.

ABSTRACT: Fitting of atomic components into electron cryo-microscopy (cryoEM) density maps is routinely used to understand the structure and function of macromolecular machines. Many fitting methods have been developed, but a standard protocol for successful fitting and assessment of fitted models has yet to be agreed upon among the experts in the field. Here, we created and tested a protocol that highlights important issues related to homology modelling, density map segmentation, rigid and flexible fitting, as well as the assessment of fits. As part of it, we use two different flexible fitting methods (Flex-EM and iMODfit) and demonstrate how combining the analysis of multiple fits and model assessment could result in an improved model. The protocol is applied to the case of the mature and empty ca

SUBMITTER: Pandurangan AP 

PROVIDER: S-EPMC3988922 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature