Machine learning in computational docking

MA Khamis, W Gomaa, WF Ahmed - Artificial intelligence in medicine, 2015 - Elsevier
machine learning (ML) techniques in computational docking. The use of smart computational
… Central to this methodology is the notion of computational docking which is the process of …

[HTML][HTML] Protein–ligand docking in the machine-learning era

C Yang, EA Chen, Y Zhang - Molecules, 2022 - mdpi.com
… Structure-based inhibitor design approaches often use molecular docking, a computational
procedure that efficiently predicts non-covalent interactions between macromolecules (…

Machine learning in computational chemistry

BB Goldman, WP Walters - Annual Reports in Computational Chemistry, 2006 - Elsevier
… of machine learning techniques that have recently appeared in the computational chemistry
… In these studies, a set of molecules is computationally docked into a protein active site. The …

Molecular insights into a mechanism of resveratrol action using hybrid computational docking/CoMFA and machine learning approach

A Pande, M Manchanda, HR Bhat… - Journal of …, 2022 - Taylor & Francis
… of computational receptor-based docking, ligand-based CoMFA/CoMSIA and Machine learning
… All computational docking, CoMFA/CoMSIA, and ML results from our current study were …

A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking

PJ Ballester, JBO Mitchell - Bioinformatics, 2010 - academic.oup.com
… Molecular docking is a computational technique … docking has two stages: docking molecules
into the target's binding site (pose identification), and predicting how strongly the docked

Modelling peptide–protein complexes: docking, simulations and machine learning

A Mondal, L Chang, A Perez - QRB discovery, 2022 - cambridge.org
… the advances in docking, molecular simulations and machine learning to tackle problems …
computational methods that are routinely used to elucidate different aspects of PPIs: 1) docking

Machine learning optimization of cross docking accuracy

EJ Bjerrum - Computational biology and chemistry, 2016 - Elsevier
docking power using a supervised machine learning approach and a manually curated
database of ligands and cross docking … in a similar docking performance with regard to docking

Improving structure-based virtual screening with ensemble docking and machine learning

J Ricci-Lopez, SA Aguila, MK Gilson… - Journal of chemical …, 2021 - ACS Publications
… its explicit representation in every docking run implies a high computational cost. Therefore,
a … is the approach known as ensemble docking. Ensemble docking consists of using a set of …

Protein docking using surface matching and supervised machine learning

AJ Bordner, AA Gorin - Proteins: Structure, Function, and …, 2007 - Wiley Online Library
… A comprehensive docking procedure is described in which … the docked conformations using
a supervised machine learningComputational docking methods, which provide structural …

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
… Therefore, the incorporation of atomic interaction features into the computational
framework presented in this paper may provide a better model of cooperativity in the future. …