HingeProt: Automated prediction of hinges in protein structures

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...

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Bibliographic Details
Published in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2008-03, Vol.70 (4), p.1219-1227
Main Authors: Emekli, Ugur, Schneidman-Duhovny, Dina, Wolfson, Haim J., Nussinov, Ruth, Haliloglu, Turkan
Format: Article
Language:English
Subjects:
Computational Biology - methods
Computer Simulation
Databases, Protein
docking
hinges
Internet
Ligands
Models, Molecular
Movement
NMA
Protein Binding
Protein Conformation
protein flexibility
protein function
Proteins - chemistry
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Summary: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/. Proteins 2008. © 2007 Wiley‐Liss, Inc.
ISSN:0887-3585
1097-0134
DOI:10.1002/prot.21613