Efficient electrostatic solvation model for protein-fragment docking
A method is presented for the fast evaluation of the binding energy of a protein‐small molecule complex with electrostatic solvation. It makes use of a fast preprocessing step based on the assumption that the main contribution to electrostatic desolvation upon ligand binding originates from the disp...
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| Veröffentlicht in: | Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2001-02, Vol.42 (2), p.256-268 |
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| container_title | Proteins, structure, function, and bioinformatics |
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| creator | Majeux, Nicolas Scarsi, Marco Caflisch, Amedeo |
| description | A method is presented for the fast evaluation of the binding energy of a protein‐small molecule complex with electrostatic solvation. It makes use of a fast preprocessing step based on the assumption that the main contribution to electrostatic desolvation upon ligand binding originates from the displacement of the first shell of water molecules. For a rigid protein, the precomputation of the energy contributions on a set of grids allows the estimation of the energy in solution of about 300 protein‐fragment binding modes per second on a personal computer. The docking procedure is applied to five rigid binding sites whose size ranges from 17 residues to a whole protein of 107 amino acids. Using a library of 70 mainly rigid molecules, known micromolar inhibitors or close analogs are docked and prioritized correctly. The docking based rank‐ordering of the library requires about 5 h and is proposed as a complementary approach to structure‐activity relationships by nuclear magnetic resonance. Proteins 2001;42:256–268. © 2000 Wiley‐Liss, Inc. |
| doi_str_mv | 10.1002/1097-0134(20010201)42:2<256::AID-PROT130>3.0.CO;2-4 |
| format | Article |
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| ispartof | Proteins, structure, function, and bioinformatics, 2001-02, Vol.42 (2), p.256-268 |
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| language | eng |
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| source | MEDLINE; Wiley Online Library Journals Frontfile Complete |
| subjects | binding energy Binding Sites Caspase 1 - chemistry first solvation shell FKBP-12 ICE library docking Ligands MDM2 Mitogen-Activated Protein Kinases - chemistry Models, Chemical Models, Molecular Nuclear Proteins p38 MAP kinase p38 Mitogen-Activated Protein Kinases Peptide Fragments - chemistry Protein Binding Proto-Oncogene Proteins - chemistry Proto-Oncogene Proteins c-mdm2 Reproducibility of Results Software Validation Static Electricity Tacrolimus Binding Protein 1A - chemistry thrombin Thrombin - chemistry |
| title | Efficient electrostatic solvation model for protein-fragment docking |
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