منابع مشابه
RESEARCH ARTICLES Ligand Solvation in Molecular Docking
Solvation plays an important role in ligand-protein association and has a strong impact on comparisons of binding energies for dissimilar molecules. When databases of such molecules are screened for complementarity to receptors of known structure, as often occurs in structure-based inhibitor discovery, failure to consider ligand solvation often leads to putative ligands that are too highly char...
متن کاملMolecular Docking with Ligand Attached Water Molecules
A novel approach to incorporate water molecules in protein-ligand docking is proposed. In this method, the water molecules display the same flexibility during the docking simulation as the ligand. The method solvates the ligand with the maximum number of water molecules, and these are then retained or displaced depending on energy contributions during the docking simulation. Instead of being a ...
متن کاملExhaustive docking of molecular fragments with electrostatic solvation.
A new method is presented for docking molecular fragments to a rigid protein with evaluation of the binding energy. Polar fragments are docked with at least one hydrogen bond with the protein while apolar fragments are positioned in the hydrophobic pockets. The electrostatic contribution to the binding energy, which consists of screened intermolecular energy and protein and fragment desolvation...
متن کاملLigand Pose and Orientational Sampling in Molecular Docking
Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavio...
متن کاملMolecular docking and ligand specificity in fragment-based inhibitor discovery.
Fragment screens have successfully identified new scaffolds in drug discovery, often with relatively high hit rates (5%) using small screening libraries (1,000-10,000 compounds). This raises two questions: would other noteworthy chemotypes be found were one to screen all commercially available fragments (>300,000), and does the success rate imply low specificity of fragments? We used molecular ...
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ژورنال
عنوان ژورنال: Proteins: Structure, Function, and Genetics
سال: 1999
ISSN: 0887-3585,1097-0134
DOI: 10.1002/(sici)1097-0134(19990101)34:1<4::aid-prot2>3.0.co;2-6