Lean-docking: exploiting ligands' predicted docking scores to accelerate molecular docking

F Berenger, A Kumar, KYJ Zhang… - Journal of Chemical …, 2021 - ACS Publications
In structure-based virtual screening (SBVS), a binding site on a protein structure is used to
search for ligands with favorable nonbonded interactions. Because it is computationally …

DOCKSTRING: easy molecular docking yields better benchmarks for ligand design

M García-Ortegón, GNC Simm, AJ Tripp… - Journal of chemical …, 2022 - ACS Publications
The field of machine learning for drug discovery is witnessing an explosion of novel
methods. These methods are often benchmarked on simple physicochemical properties …

MILCDock: machine learning enhanced consensus docking for virtual screening in drug discovery

CJ Morris, JA Stern, B Stark… - Journal of Chemical …, 2022 - ACS Publications
Molecular docking tools are regularly used to computationally identify new molecules in
virtual screening for drug discovery. However, docking tools suffer from inaccurate scoring …

Ligand pose and orientational sampling in molecular docking

RG Coleman, M Carchia, T Sterling, JJ Irwin… - PloS one, 2013 - journals.plos.org
Molecular docking remains an important tool for structure-based screening to find new
ligands and chemical probes. As docking ambitions grow to include new scoring function …

Automated docking screens: a feasibility study

JJ Irwin, BK Shoichet, MM Mysinger… - Journal of medicinal …, 2009 - ACS Publications
Molecular docking is the most practical approach to leverage protein structure for ligand
discovery, but the technique retains important liabilities that make it challenging to deploy on …

Machine‐learning scoring functions for structure‐based virtual screening

H Li, KH Sze, G Lu, PJ Ballester - Wiley Interdisciplinary …, 2021 - Wiley Online Library
Molecular docking predicts whether and how small molecules bind to a macromolecular
target using a suitable 3D structure. Scoring functions for structure‐based virtual screening …

DockOpt: A tool for automatic optimization of docking models

IS Knight, O Mailhot, KG Tang… - Journal of Chemical …, 2024 - ACS Publications
Molecular docking is a widely used technique for leveraging protein structure for ligand
discovery, but it remains difficult to utilize due to limitations that have not been adequately …

Rapid context-dependent ligand desolvation in molecular docking

MM Mysinger, BK Shoichet - Journal of chemical information and …, 2010 - ACS Publications
In structure-based screens for new ligands, a molecular docking algorithm must rapidly
score many molecules in multiple configurations, accounting for both the ligand's …

Consensus docking: improving the reliability of docking in a virtual screening context

DR Houston, MD Walkinshaw - Journal of chemical information …, 2013 - ACS Publications
Structure-based virtual screening relies on scoring the predicted binding modes of
compounds docked into the target. Because the accuracy of this scoring relies on the …

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets

WP Feinstein, M Brylinski - Journal of cheminformatics, 2015 - Springer
Background Computational approaches have emerged as an instrumental methodology in
modern research. For example, virtual screening by molecular docking is routinely used in …