@article{bibcite_135,
  keywords = {Models, Molecular, Protein Binding, Binding Sites, Ligands, Models, Chemical, Peptide Fragments, Static Electricity, Thrombin, Nuclear Proteins, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-mdm2, Caspase 1, Mitogen-Activated Protein Kinases, Reproducibility of Results, Software Validation, Tacrolimus Binding Protein 1A, p38 Mitogen-Activated Protein Kinases},
  author = {N. Majeux and M. Scarsi and A. Caflisch},
  title = {Efficient electrostatic solvation model for protein-fragment docking},
  abstract = {<p>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.</p>},
  year = {2001},
  journal = {Proteins: Structure, Function, and Bioinformatics},
  volume = {42},
  pages = {256-268},
  month = {2001 Feb 1},
  issn = {0887-3585},
  doi = {DOI: 10.1002/1097-0134(20010201)42:2<256::AID-PROT130>3.0.CO;2-4},
  language = {eng},
}