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ProPairs: A Data Set for Protein-Protein Docking.

Florian Krull1, Gerrit Korff1, Nadia Elghobashi-Meinhardt1

  • 1Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstrasse 36a, 14195 Berlin, Germany.

Journal of Chemical Information and Modeling
|June 3, 2015
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Summary
This summary is machine-generated.

ProPairs is a new dataset of protein-protein docking complexes, identified using an automated method that selects legitimate complexes and their unbound partners from the Protein Data Bank (PDB). This resource aids in studying protein-protein interactions.

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Computational Biology

Background:

  • Protein-protein interactions are crucial for cellular functions.
  • Identifying and analyzing protein complexes is essential for understanding biological processes.
  • Databases of protein structures, like the Protein Data Bank (PDB), are vital resources.

Purpose of the Study:

  • To create a curated dataset of legitimate protein-protein docking complexes and their unbound structures.
  • To develop an automated method for identifying high-quality protein-protein docking data.
  • To provide a valuable resource for researchers studying protein-protein interactions and docking.

Main Methods:

  • Utilized the Protein Data Bank (PDB) to identify biological assemblies representing protein complexes.
  • Developed an automated program (ProPairs) to select legitimate protein-protein docking complexes and their corresponding unbound structures based on specific criteria.
  • Applied sequence redundancy filtering (less than 40% sequence identity at the interface) to create a nonredundant dataset.

Main Results:

  • Identified 5,642 protein complexes, yielding 11,600 unbound protein pairs.
  • After redundancy reduction, 2,070 nonredundant protein docking complexes were obtained.
  • For 810 complexes, both docking partners had corresponding unbound structures in the PDB; 417 complexes featured a cofactor at the interface.
  • Comparison with the Protein-Protein Docking Benchmark 4.0 (DB4.0) revealed minor discrepancies, with ProPairs offering a more refined selection.

Conclusions:

  • The ProPairs dataset provides a valuable, curated collection of nonredundant protein-protein docking complexes.
  • The automated ProPairs method offers an efficient way to extract high-quality docking data from the PDB.
  • The dataset and associated code are publicly available, facilitating further research in protein-protein interactions and drug discovery.