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 …

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 …

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 …

Beware of Machine Learning-Based Scoring Functions On the Danger of Developing Black Boxes

J Gabel, J Desaphy, D Rognan - Journal of chemical information …, 2014 - ACS Publications
Training machine learning algorithms with protein–ligand descriptors has recently gained
considerable attention to predict binding constants from atomic coordinates. Starting from a …

Machine learning in computational docking

MA Khamis, W Gomaa, WF Ahmed - Artificial intelligence in medicine, 2015 - Elsevier
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 …

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 …

Decoys for docking

AP Graves, R Brenk, BK Shoichet - Journal of medicinal chemistry, 2005 - ACS Publications
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 …

Improving AutoDock Vina using random forest: the growing accuracy of binding affinity prediction by the effective exploitation of larger data sets

H Li, KS Leung, MH Wong, PJ Ballester - Molecular informatics, 2015 - Wiley Online Library
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 …

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 …

[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 …