Protein Structure Prediction pp 199-207

Part of the Methods in Molecular Biology book series (MIMB, volume 1137) | Cite as

DOCK/PIERR: Web Server for Structure Prediction of Protein–Protein Complexes

  • Shruthi Viswanath
  • D. V. S. Ravikant
  • Ron Elber
Protocol

Abstract

In protein docking we aim to find the structure of the complex formed when two proteins interact. Protein–protein interactions are crucial for cell function. Here we discuss the usage of DOCK/PIERR. In DOCK/PIERR, a uniformly discrete sampling of orientations of one protein with respect to the other, are scored, followed by clustering, refinement, and reranking of structures. The novelty of this method lies in the scoring functions used. These are obtained by examining hundreds of millions of correctly and incorrectly docked structures, using an algorithm based on mathematical programming, with provable convergence properties.

Keywords

Protein–protein docking FFT-based docking Knowledge-based potential Atomic potential Residue potential Scoring function Mathematical programming Refinement and reranking 

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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Shruthi Viswanath
    • 1
    • 2
  • D. V. S. Ravikant
    • 3
  • Ron Elber
    • 4
  1. 1.Department of Computer ScienceUniversity of Texas at AustinAustinUSA
  2. 2.Institute for Computational Engineering and SciencesUniversity of Texas at AustinAustinUSA
  3. 3.WalmartLabsSan BrunoUSA
  4. 4.Department of Chemistry and Biochemistry and Institute for Computational Engineering and SciencesUniversity of Texas at AustinAustinUSA

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