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INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool.

Chloé Dequeker1, Elodie Laine1, Alessandra Carbone1,2

  • 1UPMC-Univ P6, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative-UMR 7238, Sorbonne Universités , 4 place Jussieu, 75005 Paris, France.

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|October 10, 2017
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Summary
This summary is machine-generated.

INTerface Builder (INTBuilder) is a fast, open-source program for computing protein-protein interfaces from molecular docking outputs. It efficiently identifies interacting surfaces at residue and atom levels, supporting various input formats.

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Molecular modeling

Background:

  • Protein-protein interactions are crucial for biological processes.
  • Accurate identification of protein interfaces is essential for understanding molecular mechanisms.
  • Existing tools may lack efficiency or broad compatibility with docking software outputs.

Purpose of the Study:

  • To develop a fast and user-friendly program for computing protein-protein interfaces.
  • To enable efficient retrieval of interface data from diverse molecular docking software outputs.
  • To provide a flexible tool for analyzing protein-protein interactions at multiple resolutions.

Main Methods:

  • The INTerface Builder (INTBuilder) program was developed using C programming language.
  • The software processes outputs from popular docking programs (ATTRACT, HEX, MAXDo, ZDOCK) and standard formats like Protein Data Bank (PDB).
  • It employs an empirically determined linear complexity algorithm for efficient interface computation.

Main Results:

  • INTBuilder successfully computes protein-protein interfaces with high speed and ease of use.
  • The program accurately identifies interacting surfaces at both residue and atom resolutions.
  • It demonstrates compatibility with multiple common molecular docking software output formats.

Conclusions:

  • INTBuilder offers an efficient and versatile solution for analyzing protein-protein interfaces.
  • The open-source nature and broad compatibility make it a valuable tool for researchers in structural biology and computational chemistry.
  • This program facilitates the study of molecular recognition and complex formation.