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Template-Based Modeling of Protein Complexes Using the PPI3D Web Server.

Justas Dapkūnas1, Česlovas Venclovas2

  • 1Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.

Methods in Molecular Biology (Clifton, N.J.)
|July 5, 2020
PubMed
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Computational modeling bridges the gap between known protein-protein interactions and their structures. The PPI3D web server aids in identifying homologous complexes and modeling protein structures for improved accuracy.

Area of Science:

  • Structural Bioinformatics
  • Computational Biology
  • Protein Structure Prediction

Background:

  • A significant disparity exists between the number of identified protein-protein interactions (PPIs) and available experimentally determined complex structures.
  • Computational structure modeling, particularly template-based modeling, is crucial for predicting protein and protein complex structures.
  • Identifying suitable homologous structures for template-based modeling remains a key challenge.

Purpose of the Study:

  • To introduce the PPI3D web server, designed to simplify the identification of homologous protein complexes.
  • To provide tools for analyzing protein interactions and modeling protein complexes.
  • To demonstrate the utility of PPI3D in homology modeling of multimeric proteins.

Main Methods:

Keywords:
ClusteringDockingHomology modelingProtein complexProtein structureProtein–peptide interactionsProtein–protein interactionsStructure predictionTemplate-based modeling

Related Experiment Videos

  • Development of the PPI3D web server for searching homologous protein complexes.
  • Integration of tools for interaction analysis and protein complex modeling within the server.
  • Validation of PPI3D performance in recent CASP and CAPRI experiments.

Main Results:

  • PPI3D effectively searches for homologous protein complexes, aiding in template identification.
  • The server facilitates the analysis of identified protein-protein interactions.
  • PPI3D has been shown to be a valuable tool for homology modeling of multimeric proteins.

Conclusions:

  • The PPI3D web server addresses the challenge of template identification in homology modeling of protein complexes.
  • PPI3D offers a comprehensive solution for analyzing and modeling protein complexes.
  • The server's performance in benchmark experiments highlights its utility for structural biologists.