Protein-protein docking by simulating the process of association subject to biochemical constraints
| Autor: | Rebecca C. Wade, Peter J. Winn, Anna Feldman-Salit, Tim Johann, Ting Wang, Domantas Motiejunas, Razif R. Gabdoulline |
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| Rok vydání: | 2008 |
| Předmět: |
Databases
Factual Biochemical Phenomena Protein Conformation Molecular Sequence Data Static Electricity Crystallography X-Ray Biochemistry Models Biological Protein Structure Secondary Diffusion Molecular dynamics Protein structure Structural Biology Computational chemistry Animals Humans Computer Simulation Amino Acid Sequence Cluster analysis Molecular Biology Fourier Analysis Chemistry Protein protein Osmolar Concentration Computational Biology Proteins Hydrogen Bonding Hierarchical clustering Protein Structure Tertiary Docking (molecular) Brownian dynamics Protein–protein interaction prediction Biological system Algorithms |
| Zdroj: | Proteins. 71(4) |
| ISSN: | 1097-0134 |
| Popis: | We present a computational procedure for modeling protein-protein association and predicting the structures of protein-protein complexes. The initial sampling stage is based on an efficient Brownian dynamics algorithm that mimics the physical process of diffusional association. Relevant biochemical data can be directly incorporated as distance constraints at this stage. The docked configurations are then grouped with a hierarchical clustering algorithm into ensembles that represent potential protein-protein encounter complexes. Flexible refinement of selected representative structures is done by molecular dynamics simulation. The protein-protein docking procedure was thoroughly tested on 10 structurally and functionally diverse protein-protein complexes. Starting from X-ray crystal structures of the unbound proteins, in 9 out of 10 cases it yields structures of protein-protein complexes close to those determined experimentally with the percentage of correct contacts >30% and interface backbone RMSD |
| Databáze: | OpenAIRE |
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