Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace
N Singh, L Chaput, BO Villoutreix - Briefings in bioinformatics, 2021 - academic.oup.com
The interplay between life sciences and advancing technology drives a continuous cycle of
chemical data growth; these data are most often stored in open or partially open databases …
chemical data growth; these data are most often stored in open or partially open databases …
On exploring structure–activity relationships
R Guha - In silico models for drug discovery, 2013 - Springer
Understanding structure–activity relationships (SARs) for a given set of molecules allows
one to rationally explore chemical space and develop a chemical series optimizing multiple …
one to rationally explore chemical space and develop a chemical series optimizing multiple …
In need of bias control: evaluating chemical data for machine learning in structure-based virtual screening
Reports of successful applications of machine learning (ML) methods in structure-based
virtual screening (SBVS) are increasing. ML methods such as convolutional neural networks …
virtual screening (SBVS) are increasing. ML methods such as convolutional neural networks …
Anthropogenic biases in chemical reaction data hinder exploratory inorganic synthesis
X Jia, A Lynch, Y Huang, M Danielson, I Lang'at… - Nature, 2019 - nature.com
Most chemical experiments are planned by human scientists and therefore are subject to a
variety of human cognitive biases, heuristics and social influences. These anthropogenic …
variety of human cognitive biases, heuristics and social influences. These anthropogenic …
Most ligand-based classification benchmarks reward memorization rather than generalization
I Wallach, A Heifets - Journal of chemical information and …, 2018 - ACS Publications
Undetected overfitting can occur when there are significant redundancies between training
and validation data. We describe AVE, a new measure of training–validation redundancy for …
and validation data. We describe AVE, a new measure of training–validation redundancy for …
Computational investigations of hERG channel blockers: New insights and current predictive models
BO Villoutreix, O Taboureau - Advanced drug delivery reviews, 2015 - Elsevier
Identification of potential human Ether-a-go-go Related-Gene (hERG) potassium channel
blockers is an essential part of the drug development and drug safety process in …
blockers is an essential part of the drug development and drug safety process in …
Statistical and machine learning approaches to predicting protein–ligand interactions
LJ Colwell - Current opinion in structural biology, 2018 - Elsevier
Data driven computational approaches to predicting protein–ligand binding are currently
achieving unprecedented levels of accuracy on held-out test datasets. Up until now …
achieving unprecedented levels of accuracy on held-out test datasets. Up until now …
Complex machine learning model needs complex testing: Examining predictability of molecular binding affinity by a graph neural network
T Nikolaienko, O Gurbych… - Journal of Computational …, 2022 - Wiley Online Library
Drug discovery pipelines typically involve high‐throughput screening of large amounts of
compounds in a search of potential drugs candidates. As a chemical space of small organic …
compounds in a search of potential drugs candidates. As a chemical space of small organic …
Can machine learning predict the phase behavior of surfactants?
We explore the prediction of surfactant phase behavior using state-of-the-art machine
learning methods, using a data set for twenty-three nonionic surfactants. Most machine …
learning methods, using a data set for twenty-three nonionic surfactants. Most machine …
[HTML][HTML] Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock
Prediction of the bound configuration of small-molecule ligands that differ substantially from
the cognate ligand of a protein co-crystal structure is much more challenging than re …
the cognate ligand of a protein co-crystal structure is much more challenging than re …