A machine learning-based method to improve docking scoring functions and its application to drug repurposing
SL Kinnings, N Liu, PJ Tonge… - Journal of chemical …, 2011 - ACS Publications
Docking scoring functions are notoriously weak predictors of binding affinity. They typically
assign a common set of weights to the individual energy terms that contribute to the overall …
assign a common set of weights to the individual energy terms that contribute to the overall …
Drug efficiency indices for improvement of molecular docking scoring functions
AT García‐Sosa, C Hetényi… - Journal of computational …, 2010 - Wiley Online Library
A dataset of protein‐drug complexes with experimental binding energy and crystal structure
were analyzed and the performance of different docking engines and scoring functions (as …
were analyzed and the performance of different docking engines and scoring functions (as …
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 …
Beware of Machine Learning-Based Scoring Functions On the Danger of Developing Black Boxes
Training machine learning algorithms with protein–ligand descriptors has recently gained
considerable attention to predict binding constants from atomic coordinates. Starting from a …
considerable attention to predict binding constants from atomic coordinates. Starting from a …
Machine learning in computational docking
Objective The objective of this paper is to highlight the state-of-the-art machine learning (ML)
techniques in computational docking. The use of smart computational methods in the life …
techniques in computational docking. The use of smart computational methods in the life …
Does a more precise chemical description of protein–ligand complexes lead to more accurate prediction of binding affinity?
PJ Ballester, A Schreyer… - Journal of chemical …, 2014 - ACS Publications
Predicting the binding affinities of large sets of diverse molecules against a range of
macromolecular targets is an extremely challenging task. The scoring functions that attempt …
macromolecular targets is an extremely challenging task. The scoring functions that attempt …
Decoys for docking
Molecular docking is widely used to predict novel lead compounds for drug discovery.
Success depends on the quality of the docking scoring function, among other factors. An …
Success depends on the quality of the docking scoring function, among other factors. An …
Improving AutoDock Vina using random forest: the growing accuracy of binding affinity prediction by the effective exploitation of larger data sets
There is a growing body of evidence showing that machine learning regression results in
more accurate structure‐based prediction of protein‐ligand binding affinity. Docking …
more accurate structure‐based prediction of protein‐ligand binding affinity. Docking …
An automated strategy for binding-pose selection and docking assessment in structure-based drug design
F Ballante, GR Marshall - Journal of Chemical Information and …, 2016 - ACS Publications
Molecular docking is a widely used technique in drug design to predict the binding pose of a
candidate compound in a defined therapeutic target. Numerous docking protocols are …
candidate compound in a defined therapeutic target. Numerous docking protocols are …
[HTML][HTML] Key topics in molecular docking for drug design
PHM Torres, ACR Sodero, P Jofily… - International journal of …, 2019 - mdpi.com
Molecular docking has been widely employed as a fast and inexpensive technique in the
past decades, both in academic and industrial settings. Although this discipline has now had …
past decades, both in academic and industrial settings. Although this discipline has now had …