An Integrated Docking Pipeline for the Prediction of Large-Scale Protein-Protein Interactions

Abstract

Knowledge of the three-dimensional (3D) structures of protein complexes provides a fundamental understanding of biological systems, as well as novel insights for antimicrobial drug and vaccine design. Protein-protein docking is used to predict the 3D structures of protein complexes from their components in silico. In this study, we developed a protein-protein docking pipeline (PPDP) that integrates a variety of state-of-the-art protein docking and structure prediction techniques, providing a systematic platform to predict large-scale protein-protein interactions (PPIs). The PPDP is deployed on high performance computing (HPC) clusters, thus enabling Department of Defense scientists to harness HPC resources to investigate the PPIs of biowarfare agents for the development of countermeasures. We applied the PPDP to investigate the binding interactions of Yersinia effector proteins with their chaperone and the underlying specificity of chaperone/effector interactions.

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Document Details

Document Type
Technical Report
Publication Date
Jun 01, 2010
Accession Number
ADA549150

Entities

People

  • Anders Wallqvist
  • Kalam Kumar
  • Michael D Lee
  • Xin Hu

Organizations

  • United States Army Medical Research and Development Command

Tags

Communities of Interest

  • Biomedical

DTIC Thesaurus Topics

  • Anti-Infective Agents
  • Application Software
  • Biotechnology
  • Department Of Defense
  • Governments
  • Graphical User Interface
  • High Performance Computing
  • Molecular Biology
  • Molecular Dynamics
  • Pipelines
  • Protein-Protein Interactions
  • Scientists
  • Simulations
  • Systems Biology
  • Three Dimensional
  • User Interface

Fields of Study

  • Biology

Readers

  • Distributed Systems and Data Platform Development
  • Molecular and Cellular Biochemistry

Technology Areas

  • Biotechnology