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… GOLD has been optimised for the prediction of ligand binding positions rather than the prediction of binding affinities. It is not recommended to use scoring …
What is the difference between the GoldScore, ChemScore, ASP and ChemPLP scoring functions provided with GOLD?
… function incorporates a term, dG, that represents the total free energy change that occurs on ligand binding and was trained by regression against binding affinity …
… of protein ligand interactions. Each chromosome is assigned a fitness score based on its predicted binding affinity and the chromosomes within the population …
… Unfortunately GOLD is not ideally suited to cases where no binding site is to be designated. GOLD currently has a built-in upper limit on the maximum size …
… docking proteins are sufficiently different from those when docking ligands. In particular GOLD requires a distinct concave binding site to be defined, whereas …
… crystallographic binding pose can be reproduced better. The GOLD docking algorithm returns only very similar binding poses. If so, try using the Diverse …
… of the defined binding site the size of the ligand(s) the computer speed the GOLD configuration (e.g. docking runs that allow for flexible side chains or explicit …
… to dock if the binding site is too large or contains functionality that is not matched by equivalent functionality (donor, acceptor or hydrophobic) on the ligand …
… The default set up in the GOLD interface in CCG's MOE is designed to generate a variety of plausible and different binding poses. There are some differences …
… , 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 …
Top Support Solutions
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