HingeProt: Automated prediction of hinges in protein structures

Ugur Emekli, Dina Schneidman-Duhovny, Haim J. Wolfson, Ruth Nussinov, Turkan Haliloglu*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

185 Scopus citations

Abstract

Proteins are highly flexible molecules. Prediction of molecular flexibility aids in the comprehension and prediction of protein function and in providing details of functional mechanisms. The ability to predict the locations, directions, and extent of molecular movements can assist in fitting atomic resolution structures to low-resolution EM density maps and in predicting the complex structures of interacting molecules (docking). There are several types of molecular movements. In this work, we focus on the prediction of hinge movements. Given a single protein structure, the method automatically divides it into the rigid parts and the hinge regions connecting them. The method employs the Elastic Network Model, which is very efficient and was validated against a large data set of proteins. The output can be used in applications such as flexible protein-protein and protein-ligand docking, flexible docking of protein structures into cryo-EM maps, and refinement of low-resolution EM structures. The web server of HingeProt provides convenient visualization of the results and is available with two mirror sites at http://www.prc.boun.edu.tr/appserv/prc/ HingeProt3 and http://bioinfo3d.cs.tau.ac.il/HingeProt/.

Original languageAmerican English
Pages (from-to)1219-1227
Number of pages9
JournalProteins: Structure, Function and Genetics
Volume70
Issue number4
DOIs
StatePublished - Mar 2008
Externally publishedYes

Keywords

  • Docking
  • EM
  • Hinges
  • NMA
  • Protein flexibility
  • Protein function

Fingerprint

Dive into the research topics of 'HingeProt: Automated prediction of hinges in protein structures'. Together they form a unique fingerprint.

Cite this