Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Computational Chemistry"
DOI: 10.1002/jcc.26078
Abstract: We propose a free energy calculation method for receptor–ligand binding, which have multiple binding poses that avoids exhaustive enumeration of the poses. For systems with multiple binding poses, the standard procedure is to enumerate orientations… read more here.
Keywords: binding poses; energy; calculation; binding free ... See more keywords
Predicting binding poses and affinity ranking in D3R Grand Challenge using PL-PatchSurfer2.0
Sign Up to like & getrecommendations! Published in 2019 at "Journal of Computer-Aided Molecular Design"
DOI: 10.1007/s10822-019-00222-y
Abstract: Computational prediction of protein–ligand interactions is a useful approach that aids the drug discovery process. Two major tasks of computational approaches are to predict the docking pose of a compound in a known binding pocket… read more here.
Keywords: binding poses; challenge; affinity; predicting binding ... See more keywords
Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein–Ligand Binding Poses
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.2c01142
Abstract: Predicting the correct pose of a ligand binding to a protein and its associated binding affinity is of great importance in computer-aided drug discovery. A number of approaches have been developed to these ends, ranging… read more here.
Keywords: binding pose; ligand binding; ligand; binding poses ... See more keywords
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography
Sign Up to like & getrecommendations! Published in 2023 at "Journal of Chemical Information and Modeling"
DOI: 10.1021/acs.jcim.3c00236
Abstract: Fragment-based drug discovery has led to six approved drugs, but the small sizes of the chemical fragments used in such methods typically result in only weak interactions between the fragment and its target molecule, which… read more here.
Keywords: dynamics simulations; protein tyrosine; molecular dynamics; tyrosine phosphatase ... See more keywords
Switching of Receptor Binding Poses between Closely Related Enteroviruses
Sign Up to like & getrecommendations! Published in 2022 at "Viruses"
DOI: 10.3390/v14122625
Abstract: Echoviruses, for which there are currently no approved vaccines or drugs, are responsible for a range of human diseases, for example echovirus 11 (E11) is a major cause of serious neonatal morbidity and mortality. Decay-accelerating… read more here.
Keywords: receptor binding; switching receptor; poses closely; daf ... See more keywords