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A web interface for easy flexible protein-protein docking with ATTRACT.

Sjoerd J de Vries1, Christina E M Schindler1, Isaure Chauvot de Beauchêne1

  • 1Physics Department, Technische Universität München, Garching, Germany.

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|February 5, 2015
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Summary

This study introduces an accessible web interface for protein-protein docking using the ATTRACT program. It simplifies complex structural biology analyses for non-expert users, enabling insights into protein complex structures.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Protein-protein docking is crucial for understanding protein complex structures when experimental data is unavailable.
  • Web interfaces enhance accessibility of computational tools for structural biologists.
  • The ATTRACT program offers a robust method for protein-protein docking.

Purpose of the Study:

  • To develop an intuitive web interface for the ATTRACT protein-protein docking program.
  • To make advanced docking capabilities accessible to a broader range of users, including non-experts.
  • To support various docking scenarios, including rigid-body docking and protein flexibility.

Main Methods:

  • Development of a user-friendly web interface for the ATTRACT docking program.
  • Implementation of systematic rigid-body protein docking using the ATTRACT coarse-grained force field.
  • Integration of options to incorporate different types of protein flexibility into docking protocols.

Main Results:

  • The web interface successfully facilitates protein-protein docking using the ATTRACT program.
  • The tool supports both rigid-body docking and flexible docking approaches.
  • Docking protocols can be executed on standard desktop computers within a few hours.

Conclusions:

  • The developed web interface democratizes protein-protein docking analysis.
  • It empowers structural biologists, even those with limited computational expertise, to investigate protein complex structures.
  • This tool enhances the utility of the ATTRACT program for diverse structural biology research.