[HTML][HTML] Exponential consensus ranking improves the outcome in docking and receptor ensemble docking
Consensus-scoring methods are commonly used with molecular docking in virtual screening
campaigns to filter potential ligands for a protein target. Traditional consensus methods …
campaigns to filter potential ligands for a protein target. Traditional consensus methods …
Flexible receptor docking for drug discovery
CF Wong - Expert opinion on drug discovery, 2015 - Taylor & Francis
Introduction: Molecular docking has become a popular method for virtual screening. Docking
small molecules to a rigid biological receptor is fast but could produce many false negatives …
small molecules to a rigid biological receptor is fast but could produce many false negatives …
Supervised consensus scoring for docking and virtual screening
R Teramoto, H Fukunishi - Journal of chemical information and …, 2007 - ACS Publications
Docking programs are widely used to discover novel ligands efficiently and can predict
protein− ligand complex structures with reasonable accuracy and speed. However, there is …
protein− ligand complex structures with reasonable accuracy and speed. However, there is …
Efficient flexible backbone protein–protein docking for challenging targets
Motivation Binding-induced conformational changes challenge current computational
docking algorithms by exponentially increasing the conformational space to be explored. To …
docking algorithms by exponentially increasing the conformational space to be explored. To …
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 …
discovery, but the technique retains important liabilities that make it challenging to deploy on …
Dockey: a modern integrated tool for large-scale molecular docking and virtual screening
Molecular docking is a structure-based and computer-aided drug design approach that
plays a pivotal role in drug discovery and pharmaceutical research. AutoDock is the most …
plays a pivotal role in drug discovery and pharmaceutical research. AutoDock is the most …
DeepBSP—a machine learning method for accurate prediction of protein–ligand docking structures
J Bao, X He, JZH Zhang - Journal of chemical information and …, 2021 - ACS Publications
In recent years, machine-learning-based scoring functions have significantly improved the
scoring power. However, many of these methods do not perform well in distinguishing the …
scoring power. However, many of these methods do not perform well in distinguishing the …
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design
The field of machine learning for drug discovery is witnessing an explosion of novel
methods. These methods are often benchmarked on simple physicochemical properties …
methods. These methods are often benchmarked on simple physicochemical properties …
Improving protein-ligand docking results with high-throughput molecular dynamics simulations
H Guterres, W Im - Journal of chemical information and modeling, 2020 - ACS Publications
Structure-based virtual screening relies on classical scoring functions that often fail to
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …
reliably discriminate binders from nonbinders. In this work, we present a high-throughput …
[HTML][HTML] 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 …