ITScorePro: An Efficient Scoring Program for Evaluating the Energy Scores of Protein Structures for Structure Prediction

  • Sheng-You Huang
  • Xiaoqin Zou
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1137)

Abstract

One important component in protein structure prediction is to evaluate the free energy of a given conformation. Given the enormous number of possible conformations for a sequence, it is extremely challenging to quickly and accurately score the energies of these conformations and predict a reasonable structure within a practical computational time. Here, we describe an efficient program for energy evaluation, referred to as ITScorePro (Copyright © 2012). The energy scoring function in the ITScorePro program is based on the distance-dependent, pairwise atomic potentials for protein structure prediction that we recently derived by using statistical mechanics principles (Huang and Zou, Proteins 79:2648–2661, 2011). ITScorePro is a stand-alone program and can also be easily implemented in other software suites for protein structure prediction.

Keywords

Protein structure prediction Scoring function Free energy Statistical potentials Knowledge-based 

Notes

Acknowledgments

X.Z. is supported by NIH grant R21GM088517, NSF CAREER Award DBI-0953839, the Research Board Award RB-07-32 and the Research Council Grant URC 09-004 of the University of Missouri. The computations were performed on the HPC resources at the University of Missouri Bioinformatics Consortium (UMBC).

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Sheng-You Huang
    • 1
    • 2
  • Xiaoqin Zou
    • 1
    • 2
  1. 1.Department of Physics and Astronomy, Dalton Cardiovascular Research Center, Informatics InstituteUniversity of MissouriColumbiaUSA
  2. 2.Department of Biochemistry, Dalton Cardiovascular Research Center, Informatics InstituteUniversity of MissouriColumbiaUSA

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