Integrative computational modeling of protein interactions
- 26 March 2014
- journal article
- review article
- Published by Wiley in The FEBS Journal
- Vol. 281 (8), 1988-2003
- https://doi.org/10.1111/febs.12771
Abstract
Protein interactions define the homeostatic state of the cell. Our ability to understand these interactions and their role in both health and disease is tied to our knowledge of the 3D atomic structure of the interacting partners and their complexes. Despite advances in experimental method of structure determination, the majority of known protein interactions are still missing an atomic structure. High-resolution methods such as X-ray crystallography and NMR spectroscopy struggle with the high-throughput demand, while low-resolution techniques such as cryo-electron microscopy or small-angle X-ray scattering provide data that are too coarse. Computational structure prediction of protein complexes, or docking, was first developed to complement experimental research and has since blossomed into an independent and lively field of research. Its most successful products are hybrid approaches that combine powerful algorithms with experimental data from various sources to generate high-resolution models of protein complexes. This minireview introduces the concept of docking and docking with the help of experimental data, compares and contrasts the available integrative docking methods, and provides a guide for the experimental researcher for what types of data and which particular software can be used to model a protein complex.Keywords
This publication has 102 references indexed in Scilit:
- Mechanism of nitric oxide synthase regulation: Electron transfer and interdomain interactionsCoordination Chemistry Reviews, 2012
- Integrating atom‐based and residue‐based scoring functions for protein–protein dockingProtein Science, 2011
- Protein-Protein Complex Structure Predictions by Multimeric Threading and Template RecombinationStructure, 2011
- Protein–protein HADDocking using exclusively pseudocontact shiftsJournal of Biomolecular NMR, 2011
- SymmRef: A flexible refinement method for symmetric multimersProteins-Structure Function and Bioinformatics, 2011
- Interactome Networks and Human DiseaseCell, 2011
- Unmet challenges of structural genomicsCurrent Opinion in Structural Biology, 2010
- Solution Structure of the 128 kDa Enzyme I Dimer from Escherichia coli and Its 146 kDa Complex with HPr Using Residual Dipolar Couplings and Small- and Wide-Angle X-ray ScatteringJournal of the American Chemical Society, 2010
- An integrated suite of fast docking algorithmsProteins-Structure Function and Bioinformatics, 2010
- Convergence and combination of methods in protein–protein dockingCurrent Opinion in Structural Biology, 2009