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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Software and Databases for Protein-Protein Docking.

Małgorzata Jarończyk1, Ruben Abagyan2, Maxim Totrov3

  • 1National Medicines Institute, Warsaw, Poland.

Methods in Molecular Biology (Clifton, N.J.)
|July 10, 2024
PubMed
Summary
This summary is machine-generated.

Protein-protein interactions (PPIs) are crucial for understanding biology and disease. This chapter summarizes computational protein-protein docking software and databases for predicting these interactions.

Keywords:
Fast Fourier transformMonte CarloPPIProtein bioinformaticsProtein databasesProtein–protein dockingProtein–protein interactionsProtein–protein interface

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Area of Science:

  • Computational biology
  • Structural biology
  • Bioinformatics

Background:

  • Protein-protein interactions (PPIs) are fundamental to biological processes.
  • Understanding PPIs is key to deciphering disease mechanisms.
  • Computational methods, like protein-protein docking, aid in predicting PPIs.

Purpose of the Study:

  • To provide a comprehensive summary of software and databases for protein-protein docking.
  • To highlight tools for computational prediction of PPIs.

Main Methods:

  • Review and compilation of existing protein-protein docking software.
  • Cataloging relevant databases for docking studies.

Main Results:

  • A curated list of available protein-protein docking tools.
  • An overview of databases supporting PPI prediction.

Conclusions:

  • Protein-protein docking software and databases are essential resources for researchers.
  • These tools facilitate the study of biological systems and disease.