A practical guide to large-scale docking
Abstract Structure-based docking screens of large compound libraries have become
common in early drug and probe discovery. As computer efficiency has improved and …
common in early drug and probe discovery. As computer efficiency has improved and …
Protein–ligand docking in the machine-learning era
Molecular docking plays a significant role in early-stage drug discovery, from structure-
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …
based virtual screening (VS) to hit-to-lead optimization, and its capability and predictive …
[HTML][HTML] Structure of a hallucinogen-activated Gq-coupled 5-HT2A serotonin receptor
Hallucinogens like lysergic acid diethylamide (LSD), psilocybin, and substituted N-benzyl
phenylalkylamines are widely used recreationally with psilocybin being considered as a …
phenylalkylamines are widely used recreationally with psilocybin being considered as a …
Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor
Because nonopioid analgesics are much sought after, we computationally docked more
than 301 million virtual molecules against a validated pain target, the α2A-adrenergic …
than 301 million virtual molecules against a validated pain target, the α2A-adrenergic …
Comparative assessment of scoring functions: the CASF-2016 update
In structure-based drug design, scoring functions are often employed to evaluate protein–
ligand interactions. A variety of scoring functions have been developed so far, and thus …
ligand interactions. A variety of scoring functions have been developed so far, and thus …
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2
S Gahbauer, GJ Correy, M Schuller… - Proceedings of the …, 2023 - National Acad Sciences
The nonstructural protein 3 (NSP3) of the severe acute respiratory syndrome-coronavirus-2
(SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for …
(SARS-CoV-2) contains a conserved macrodomain enzyme (Mac1) that is critical for …
DockRMSD: an open-source tool for atom mapping and RMSD calculation of symmetric molecules through graph isomorphism
Abstract Comparison of ligand poses generated by protein–ligand docking programs has
often been carried out with the assumption of direct atomic correspondence between ligand …
often been carried out with the assumption of direct atomic correspondence between ligand …
Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) macrodomain within
the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate …
the nonstructural protein 3 counteracts host-mediated antiviral adenosine diphosphate …
DOCK 6: Impact of new features and current docking performance
This manuscript presents the latest algorithmic and methodological developments to the
structure‐based design program DOCK 6.7 focused on an updated internal energy function …
structure‐based design program DOCK 6.7 focused on an updated internal energy function …
Vinardo: A scoring function based on autodock vina improves scoring, docking, and virtual screening
R Quiroga, MA Villarreal - PloS one, 2016 - journals.plos.org
Autodock Vina is a very popular, and highly cited, open source docking program. Here we
present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based …
present a scoring function which we call Vinardo (Vina RaDii Optimized). Vinardo is based …