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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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HOMCOS: an updated server to search and model complex 3D structures.

Takeshi Kawabata1

  • 1Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan. kawabata@protein.osaka-u.ac.jp.

Journal of Structural and Functional Genomics
|August 15, 2016
PubMed
Summary
This summary is machine-generated.

The updated HOMCOS server now models and searches 3D complexes for all PDB molecules, including proteins, nucleic acids, and compounds. It predicts protein-protein and protein-compound interactions, aiding in structural analysis and mutation effect annotation.

Keywords:
BLASTComplexKCOMBUTemplate-based modeling

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Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • The Protein Data Bank (PDB) contains a vast collection of 3D molecular structures.
  • Understanding the interactions between different molecules (proteins, nucleic acids, compounds, ions) is crucial for biological research.
  • Existing tools may have limitations in comprehensively analyzing diverse molecular complexes.

Purpose of the Study:

  • To update and enhance the HOMCOS server for comprehensive analysis of 3D molecular complexes within the PDB.
  • To provide robust services for modeling protein multimers and protein-compound interactions.
  • To enable prediction of interacting molecules for query proteins and compounds.

Main Methods:

  • The HOMCOS server integrates BLAST and KCOMBU for similarity searches.
  • Sequence-replaced modeling is employed for generating structural models of complexes.
  • Flexible superposition using fkcombu is used for compound docking.
  • Template-based docking is performed for monomeric query structures.
  • Homology searching identifies potential interacting partners for query molecules.

Main Results:

  • The updated HOMCOS server now includes all PDB molecules: proteins, nucleic acids, small compounds, and metal ions.
  • Five distinct services are available: Homo Protein Multimer Modeling, Hetero Protein Multimer Modeling, Protein-Compound Complex Modeling, Searching Contact Molecules for a Query Protein, and Searching Contact Molecules for a Query Compound.
  • Results are presented in user-friendly formats like "Summary Bars" and "Site Tables", with the latter facilitating mutation effect annotation.

Conclusions:

  • The enhanced HOMCOS server offers a powerful and integrated platform for exploring and modeling diverse molecular interactions.
  • It facilitates the prediction of binding partners and the analysis of complex structural relationships.
  • The server's capabilities support various research applications, from structural biology to drug discovery and mutation analysis.