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… , requires a prepared protein input file and a fully defined binding site (preferably the same definition that was used for the original docking). The ligand(s …
… should be a H-bond acceptor. The protein atom should be available for ligand binding (e.g. solvent accessible). You can see if the atoms involved in your H-bond …
… , 1999 [DOI: 10.1006/jmbi.1999.2809] SuperStar: Improved knowledge-based interaction fields for protein binding sites M. L. Verdonk, J. C. Cole, P. Watson, V. Gillet …
… Although GOLD was designed to dock flexible ligands into protein binding sites, it is possible to perform a rigid ligand docking. To enable this option, go …
… program can then be used to predict the binding mode of the ligand and a comparison made with the crystallographically observed position. Using this methodology …
… containing a list of residues When using a list of residues to define the binding site the file must be in the following format: > HIS69 ARG71 GLU72 ARG127 ASN144 …
… How can I calculate a score per binding site residue? …
… . The starting positions of Ser, Thr and Tyr OH groups and Lys NH3+ groups therefore do not matter. In cases where you are docking a ligand into a binding site …
… useful probes to start exploring a binding site are usually: Alcohol Oxygen: the hydroxyl group can both donate and accept hydrogen bonds, so favorable spots …
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