CM2D3: Furnishing the Human Interactome with Structural Models of Protein Complexes Derived by Comparative Modeling and Docking

Patricia Mirela Bota, Altair C. Hernandez, Joan Segura, Oriol Gallego, Baldo Oliva*, Narcis Fernandez-Fuentes

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

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The human interactome is composed of around half a million interactions according to recent estimations and it is only for a small fraction of those that three-dimensional structural information is available. Indeed, the structural coverage of the human interactome is very low and given the complexity and time-consuming requirements of solving protein structures this problem will remain for the foreseeable future. Structural models, or predictions, of protein complexes can provide valuable information when the experimentally determined 3D structures are not available. Here we present CM2D3, a relational database containing structural models of the whole human interactome derived both from comparative modeling and data-driven docking. Starting from a consensus interactome derived from integrating several interactomics databases, a strategy was devised to derive structural models by computational means. Currently, CM2D3 includes 33338 structural models of which 5121 derived from comparative modeling and the remaining from docking. Of the latter, the structures of 14554 complexes were derived from monomers modeled by M4T while the rest were modeled with structures as predicted by AlphaFold2. Lastly, CM2D3 complements existing resources by focusing on models derived from both free-docking, as opposed to template-based docking, and hence expanding the available structural information on protein complexes to the scientific community.
Original languageEnglish
Article number168055
JournalJournal of Molecular Biology
Issue number14
Early online date24 Jun 2023
Publication statusPublished - 15 Jul 2023


  • comparative modeling
  • database
  • human interactome
  • protein complexes
  • protein docking
  • structural models
  • Protein Interaction Mapping/methods
  • Humans
  • Computational Biology/methods
  • Proteins/chemistry
  • Databases, Protein
  • Protein Binding
  • Protein Conformation
  • Molecular Docking Simulation
  • Software


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