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The MultiBac Protein Complex Production Platform at the EMBL
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ProteinFishing: a protein complex generator within the ModelX toolsuite.

Damiano Cianferoni1, Leandro G Radusky1, Sarah A Head1

  • 1Systems Biology, Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona 08003, Spain.

Bioinformatics (Oxford, England)
|May 22, 2020
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Summary
This summary is machine-generated.

ProteinFishing generates accurate 3D protein-protein interaction models using backbone compatibility and a statistical force field. This tool aids in designing protein complexes when experimental data is unavailable.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Accurate 3D modeling of protein-protein interactions (PPI) is crucial for understanding biological processes.
  • Experimental determination of complex structures is often challenging and time-consuming.
  • There is a need for computational tools to predict and model PPIs at atomic resolution.

Purpose of the Study:

  • To introduce ProteinFishing, a novel tool within the ModelX toolsuite for generating 3D protein complexes.
  • To enable the design of protein interfaces by predicting alternative PPIs.
  • To provide accurate atomic-level models of protein complexes.

Main Methods:

  • ProteinFishing utilizes backbone compatibility of protein fragments to generate mutually exclusive protein interfaces.
  • A knowledge-based statistical force field is employed for rapid evaluation of generated interfaces.
  • The algorithm was tested using interleukin-10-R2, interferon-lambda-3, and a database of interleukin-10 X-ray structures.

Main Results:

  • ProteinFishing successfully generated structural models of interleukin-10-R2/interleukin-10.
  • The generated models showed agreement with experimental data.
  • The tool demonstrates the capability to propose known and putative alternative 3D PPIs.

Conclusions:

  • ProteinFishing is an effective tool for generating accurate 3D models of protein complexes.
  • The tool aids in protein interface design and structural modeling.
  • It provides a valuable resource for researchers studying protein-protein interactions.