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

Bioinformatics. 2012 Sep 15;28(18):2391-3. doi: 10.1093/bioinformatics/bts446. Epub 2012 Jul 12.


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.

Availability: The RIBFIND web server and its standalone program are available at http://ribfind.ismb.lon.ac.uk.

Contact: a.pandurangan@mail.cryst.bbk.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cryoelectron Microscopy*
  • Escherichia coli Proteins / chemistry
  • Internet
  • Periplasmic Binding Proteins / chemistry
  • Protein Structure, Secondary*
  • Software*


  • Escherichia coli Proteins
  • Periplasmic Binding Proteins
  • RbsB protein, E coli