An Open-Source Implementation of the Scaffold Identification and Naming System (SCINS) and Example Applications.
KP Petrov, A Bender
– Journal of chemical information and modeling
(2024)
64,
7905
(DOI: 10.1021/acs.jcim.4c01314)
Prediction of Inhibitory Activity Against the MATE1 Transporter via Combined Fingerprint- and Physics-Based Machine Learning Models
K Handa, S Sasaki, S Asano, M Kageyama, T Iijima, A Bender
– Journal of Chemical Information and Modeling
(2024)
64,
7068
(DOI: 10.1021/acs.jcim.4c00921)
Improved Detection of Drug-Induced Liver Injury by Integrating Predicted <i>In Vivo</i> and <i>In Vitro</i> Data.
S Seal, D Williams, L Hosseini-Gerami, M Mahale, AE Carpenter, O Spjuth, A Bender
– Chem Res Toxicol
(2024)
37,
1290
Step Forward Cross Validation for Bioactivity Prediction: Out of Distribution Validation in Drug Discovery.
US Saha, M Vendruscolo, AE Carpenter, S Singh, A Bender, S Seal
(2024)
(DOI: 10.1101/2024.07.02.601740)
Calibrated prediction of scarce adverse drug reaction labels with conditional neural processes
M Garcia-Ortegon, S Seal, S Singh, A Bender, S Bacallado
(2024)
(DOI: 10.1101/2024.06.07.598036)
Improved Detection of Drug-Induced Liver Injury by Integrating Predicted in vivo and in vitro Data
S Seal, DP Williams, L Hosseini-Gerami, M Mahale, AE Carpenter, O Spjuth, A Bender
(2024)
(DOI: 10.1101/2024.01.10.575128)
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.
S Seal, M-A Trapotsi, O Spjuth, S Singh, J Carreras-Puigvert, N Greene, A Bender, AE Carpenter
(2024)
(DOI: 10.1101/2024.05.04.592531)
A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.
S Seal, M-A Trapotsi, O Spjuth, S Singh, J Carreras-Puigvert, N Greene, A Bender, AE Carpenter
– ArXiv
(2024)
PKSmart: An Open-Source Computational Model to Predict in vivo Pharmacokinetics of Small Molecules
S Seal, M-A Trapotsi, V Subramanian, O Spjuth, N Greene, A Bender
(2024)
(DOI: 10.1101/2024.02.02.578658)
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA Drug-Induced Cardiotoxicity Rank
S Seal, O Spjuth, L Hosseini-Gerami, M García-Ortegón, S Singh, A Bender, AE Carpenter
– J Chem Inf Model
(2024)
64,
1172
(DOI: 10.1021/acs.jcim.3c01834)
From pixels to phenotypes: Integrating image-based profiling with cell health data as BioMorph features improves interpretability.
S Seal, J Carreras-Puigvert, S Singh, AE Carpenter, O Spjuth, A Bender
– Molecular Biology of the Cell
(2024)
35,
mr2
(DOI: 10.1091/mbc.E23-08-0298)
Applying atomistic neural networks to bias conformer ensembles towards bioactive-like conformations
B Baillif, J Cole, I Giangreco, P McCabe, A Bender
– Journal of cheminformatics
(2023)
15,
124
(DOI: 10.1186/s13321-023-00794-w)
On the difficulty of validating molecular generative models realistically: a case study on public and proprietary data
K Handa, MC Thomas, M Kageyama, T Iijima, A Bender
– Journal of Cheminformatics
(2023)
15,
112
(DOI: 10.1186/s13321-023-00781-1)
Insights into Drug Cardiotoxicity from Biological and Chemical Data: The First Public Classifiers for FDA DICTrank
S Seal, O Spjuth, L Hosseini-Gerami, M García-Ortegón, S Singh, A Bender, AE Carpenter
(2023)
(DOI: 10.1101/2023.10.15.562398)
MAVEN: Compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny
L Hosseini-Gerami, R Hernansaiz Ballesteros, A Liu, H Broughton, DA Collier, A Bender
– BMC Bioinformatics
(2023)
24,
344
(DOI: 10.1186/s12859-023-05416-8)
Editorial overview: Artificial intelligence (AI) methodology in structural biology
A Bender, C de Graaf, NM O'Boyle
– Current opinion in structural biology
(2023)
82,
102676
(DOI: 10.1016/j.sbi.2023.102676)
From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability
S Seal, J Carreras-Puigvert, A Carpenter, O Spjuth, A Bender
(2023)
(DOI: 10.1101/2023.07.14.549031)
Merging bioactivity predictions from cell morphology and chemical fingerprint models using similarity to training data
S Seal, H Yang, M-A Trapotsi, S Singh, J Carreras-Puigvert, O Spjuth, A Bender
– J Cheminform
(2023)
15,
56
(DOI: 10.1186/s13321-023-00723-x)
Explaining Blood–Brain Barrier Permeability of Small Molecules by Integrated Analysis of Different Transport Mechanisms
FMG Cornelissen, G Markert, G Deutsch, M Antonara, N Faaij, I Bartelink, D Noske, WP Vandertop, A Bender, BA Westerman
– J Med Chem
(2023)
66,
7253
(DOI: 10.1021/acs.jmedchem.2c01824)
Prediction of Compound Plasma Concentration-Time Profiles in Mice Using Random Forest.
K Handa, P Wright, S Yoshimura, M Kageyama, T Iijima, A Bender
– Molecular Pharmaceutics
(2023)
20,
3060