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In silico prediction of P-glycoprotein binding: Insights from molecular docking studies
(Bentham Science Publishers, 2019)
Molecular Dynamics in Mixed Solvents Reveals Protein-Ligand Interactions, Improves Docking, and Allows Accurate Binding Free Energy Predictions
(American Chemical Society, 2017-04)
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has ...
Ligand and decoy sets for docking to G protein-coupled receptors
(American Chemical Society, 2012-01)
We compiled a G protein-coupled receptor (GPCR) ligand library (GLL) for 147 targets, selecting for each ligand 39 decoy molecules, collected in the GPCR Decoy Database (GDD). Decoys were chosen ensuring a ligand-decoy ...
Computational Biology Tools for Identifying Specific Ligand Binding Residues for Novel Agrochemical and Drug Design
(Bentham Science Publ Ltd, 2015-01-01)
The term agrochemicals is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, ...
Computational biology tools for identifying specific ligand binding residues for novel agrochemical and drug design
(2015-01-01)
The term “agrochemicals” is used in its generic form to represent a spectrum of pesticides, such as insecticides, fungicides or bactericides. They contain active components designed for optimized pest management and control, ...
Exponential consensus ranking improves the outcome in docking and receptor ensemble docking
(Nature Publishing Group, 2019-03)
Consensus-scoring methods are commonly used with molecular docking in virtual screening campaigns to filter potential ligands for a protein target. Traditional consensus methods combine results from different docking ...
AutoDock Bias: improving binding mode prediction and virtual screening using known protein–ligand interactions
(Oxford University Press, 2019-10)
Summary: The performance of docking calculations can be improved by tuning parameters for the system of interest, e.g. biasing the results towards the formation of relevant protein-ligand interactions, such as known ligand ...
Solvent structure improves docking prediction in lectin-carbohydrate complexes
(Oxford University Press, 2013-02)
Recognition and complex formation between proteins and carbohydrates is a key issue in many important biological processes. Determination of the three-dimensional structure of such complexes is thus most relevant, but ...