RIBFIND: A web server for identifying rigid bodies in protein structures and to aid flexible fitting into cryo EM maps

Abstract

Motivation: To better analyze low-resolution cryo electron microscopy maps of macromolecular assemblies, component atomic structures frequently have to be flexibly fitted into them. Reaching an optimal fit and preventing the fitting process from getting trapped in local minima can be significantly improved by identifying appropriate rigid bodies (RBs) in the fitted component. Results: Here we present the RIBFIND server, a tool for identifying RBs in protein structures. The server identifies RBs in proteins by calculating spatial proximity between their secondary structural elements. © The Author 2012. Published by Oxford University Press. All rights reserved.