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HingeProt: Automated prediction of hinges in protein structures

Authors

  • Ugur Emekli,

    1. Polymer Research Center and Chemical Engineering Department, Bogaziçi University, 34342 Bebek, Istanbul, Turkey
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  • Dina Schneidman-Duhovny,

    1. School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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  • Haim J. Wolfson,

    1. School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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  • Ruth Nussinov,

    1. Basic Research Program, SAIC-Frederick Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, Maryland 21701
    2. Department of Human Genetics and Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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  • Turkan Haliloglu

    Corresponding author
    1. Polymer Research Center and Chemical Engineering Department, Bogaziçi University, 34342 Bebek, Istanbul, Turkey
    • Polymer Research Center and Chemical Engineering Department, Bogaziçi University, 34342 Bebek, Istanbul, Turkey
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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/. Proteins 2008. © 2007 Wiley-Liss, Inc.

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