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Abstract
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 language | English |
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Article number | 168055 |
Journal | Journal of Molecular Biology |
Volume | 435 |
Issue number | 14 |
Early online date | 24 Jun 2023 |
DOIs | |
Publication status | Published - 15 Jul 2023 |
Keywords
- 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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- 1 Finished
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BBSRC Core Strategic Programme in Resilient Crops: Grasslands Gogerddan
Armstead, I. (PI), Donnison, I. (CoI), Jones, H. (CoI), Skot, L. (CoI), Fernandez Fuentes, N. (CoI), Phillips, D. (PI), Kingston-Smith, A. (CoI) & Bosch, M. (CoI)
Biotechnology and Biological Sciences Research Council
01 Apr 2017 → 31 Mar 2020
Project: Externally funded research