… more robust physical models. The structure-guided models accurately predict binding affinities
over a … of the protein pockets and ligand binding modes. Structure-guidance for the QMOD …

… This method was used to predict binding affinities for a test … [40] is an approach to dock
ligands into protein models that do … Structureguided docking methods make use of information …

… within the ATP binding pocket, we found … affinity loss to 5-fold (ΔΔG = 0.95 Kcal/mol), the
model was able to detect five out of six resistance cases of E255 mutations, while still predicting …

… into larger molecules with higher affinity and potency. These … workers showed that
pocket-finding algorithms predict marked … at the interface, the authors also include in the model …

… predicted to enlarge the binding pocket as rifampicin does. The analogs showed a marked
decrease in PXR binding affinity … validating our structural prediction in a cellular model. The …

… constructs a three-dimensional model of a given protein … Comparative modeling methods
and structureguided design … of comparative models is to rationalize trends in binding affinities …

… of the effect of protein mutations, and structure-guided virtual … for predicting the binding
affinity between a model structure … of loop regions in the catalytic pocket of inactive kinases are …

… to maximize the predicted on-target binding affinity of generated … pocket) such that it additionally
informs the GMD model of … optimizing the predicted activity according to a QSAR model. …

… displaying high in silico binding affinity for the DENV protease … was predicted to interact
with Asp129 of the S1 pocket via … In summary, our combined approach of homology modeling, …

… A structure-guided approach for protein pocket modeling and affinity prediction. Journal
of Computer-Aided Molecular Design 2013, 27 (11) , 917-934. https://doi.org/10.1007/s10822-…