Introduction

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/.

Publications

  1. HingeProt: automated prediction of hinges in protein structures.
    Cite this
    Emekli U, Schneidman-Duhovny D, Wolfson HJ, Nussinov R, Haliloglu T, 2008-03-01 - Proteins

Credits

  1. Ugur Emekli
    Developer

    Polymer Research Center and Chemical Engineering Department, Bogaziçi University, Turkey

  2. Dina Schneidman-Duhovny
    Developer

  3. Haim J Wolfson
    Developer

  4. Ruth Nussinov
    Developer

  5. Turkan Haliloglu
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT000336
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByTurkan Haliloglu