Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

Irina Kufareva, Manuel Rueda, Vsevolod Katritch, GPCR Dock 2010 participants, Raymond C Stevens, Ruben Abagyan

Research output: Contribution to journalArticle

229 Citations (Scopus)

Abstract

The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule antagonists and CXCR4 with a synthetic cyclopeptide. Thirty-five groups submitted their receptor-ligand complex structure predictions prior to the release of the crystallographic coordinates. With closely related homology modeling templates, as for dopamine D3 receptor, and with incorporation of biochemical and QSAR data, modern computational techniques predicted complex details with accuracy approaching experimental. In contrast, CXCR4 complexes that had less-characterized interactions and only distant homology to the known GPCR structures still remained very challenging. The assessment results provide guidance for modeling and crystallographic communities in method development and target selection for further expansion of the structural coverage of the GPCR universe.
Original languageEnglish
Pages (from-to)1108-1126
Number of pages19
JournalStructure
Volume19
Issue number8
Early online date09 Aug 2011
DOIs
Publication statusPublished - 10 Aug 2011

Bibliographical note

Copyright © 2011 Elsevier Ltd. All rights reserved.

Keywords

  • Amino Acid Sequence
  • Binding Sites
  • Computer Simulation
  • Crystallography, X-Ray
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Peptide Fragments
  • Protein Binding
  • Receptors, CXCR4
  • Receptors, Dopamine D3
  • Receptors, G-Protein-Coupled
  • Salicylamides
  • Thiourea

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    Kufareva, I., Rueda, M., Katritch, V., GPCR Dock 2010 participants, Stevens, R. C., & Abagyan, R. (2011). Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure, 19(8), 1108-1126. https://doi.org/10.1016/j.str.2011.05.012