Molecular docking: a powerful approach for structure-based drug discovery
Molecular docking has become an increasingly important tool for drug discovery. In this
review, we present a brief introduction of the available molecular docking methods, and their …
review, we present a brief introduction of the available molecular docking methods, and their …
The many roles of computation in drug discovery
WL Jorgensen - Science, 2004 - science.org
The Many Roles of Computation in Drug Discovery | Science news careers commentary
Journals Science Science brought to you byGoogle Indexer Log in science science …
Journals Science Science brought to you byGoogle Indexer Log in science science …
Classification of current scoring functions
J Liu, R Wang - Journal of chemical information and modeling, 2015 - ACS Publications
Scoring functions are a class of computational methods widely applied in structure-based
drug design for evaluating protein–ligand interactions. Dozens of scoring functions have …
drug design for evaluating protein–ligand interactions. Dozens of scoring functions have …
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
New empirical scoring functions have been developed to estimate the binding affinity of a
given protein-ligand complex with known three-dimensional structure. These scoring …
given protein-ligand complex with known three-dimensional structure. These scoring …
Ligand-binding affinity estimates supported by quantum-mechanical methods
U Ryde, P Soderhjelm - Chemical Reviews, 2016 - ACS Publications
One of the largest challenges of computational chemistry is calculation of accurate free
energies for the binding of a small molecule to a biological macromolecule, which has …
energies for the binding of a small molecule to a biological macromolecule, which has …
Combining docking and molecular dynamic simulations in drug design
H Alonso, AA Bliznyuk… - Medicinal research reviews, 2006 - Wiley Online Library
A rational approach is needed to maximize the chances of finding new drugs, and to exploit
the opportunities of potential new drug targets emerging from genomic and proteomic …
the opportunities of potential new drug targets emerging from genomic and proteomic …
Approaches to the description and prediction of the binding affinity of small‐molecule ligands to macromolecular receptors
The influence of a xenobiotic compound on an organism is usually summarized by the
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …
expression biological activity. If a controlled, therapeutically relevant, and regulatory action …
Comparative assessment of scoring functions on a diverse test set
Scoring functions are widely applied to the evaluation of protein− ligand binding in structure-
based drug design. We have conducted a comparative assessment of 16 popular scoring …
based drug design. We have conducted a comparative assessment of 16 popular scoring …
OPLS all-atom model for amines: resolution of the amine hydration problem
RC Rizzo, WL Jorgensen - Journal of the American chemical …, 1999 - ACS Publications
Classical force-field parameters have been developed for amines primarily by fitting to
experimental data for pure liquids and to hydrogen-bond strengths from gas-phase ab initio …
experimental data for pure liquids and to hydrogen-bond strengths from gas-phase ab initio …
Prediction of properties from simulations: free energies of solvation in hexadecane, octanol, and water
EM Duffy, WL Jorgensen - Journal of the American Chemical …, 2000 - ACS Publications
Monte Carlo (MC) statistical mechanics simulations have been carried out for more than 200
organic solutes, including 125 drugs and related heterocycles, in aqueous solution. The …
organic solutes, including 125 drugs and related heterocycles, in aqueous solution. The …