Binding Mode and Induced Fit Predictions for Prospective Computational Drug Design
2016
Computer-
aided drugdesign plays an important role in
medicinal chemistryto obtain insights into molecular mechanisms and to prioritize design strategies. Although significant improvement has been made in structure based design, it still remains a key challenge to accurately model and predict induced fit mechanisms. Most of the current available techniques either do not provide sufficient protein conformational sampling or are too computationally demanding to fit an industrial setting. The current study presents a systematic and exhaustive investigation of predicting binding modes for a range of systems using PELE (Protein
Energy LandscapeExploration), an efficient and fast
protein–ligandsampling algorithm. The systems analyzed (cytochrome P, kinase, protease, and nuclear
hormone receptor) exhibit different complexities of ligand induced fit mechanisms and
protein dynamics. The results are compared with results from classical molecular dynamics simulations and (induced fit) docking. This study shows th...
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