Synthesis and Inhibitory Assessment of ACE2 Inhibitors for SARS-CoV-2: An <i>In Silico</i> and <i>In Vitro</i> Study
X Wang, J He, L Hosseini-Gerami, M Thomas, S Thompson, J Ford, S Ortalli, Z Chen, G Destro, A Bender, F Aigbirhio, V Gouverneur
– The Journal of Organic Chemistry
(2025)
acs.joc.5c00918
(DOI: 10.1021/acs.joc.5c00918)
Identification of nanomolar adenosine A2A receptor ligands using reinforcement learning and structure-based drug design
M Thomas, PG Matricon, RJ Gillespie, M Napiórkowska, H Neale, JS Mason, J Brown, K Harwood, C Fieldhouse, NA Swain, T Geng, NM O’Boyle, F Deflorian, A Bender, C de Graaf
– Nature communications
(2025)
16,
5485
(DOI: 10.1038/s41467-025-60629-0)
Machine Learning for Toxicity Prediction Using Chemical Structures: Pillars for Success in the Real World.
S Seal, M Mahale, M García-Ortegón, CK Joshi, L Hosseini-Gerami, A Beatson, M Greenig, M Shekhar, A Patra, C Weis, A Mehrjou, A Badré, B Paisley, R Lowe, S Singh, F Shah, B Johannesson, D Williams, D Rouquie, DA Clevert, P Schwab, N Richmond, CA Nicolaou, RJ Gonzalez, R Naven, C Schramm, LR Vidler, K Mansouri, WP Walters, DD Wilk, O Spjuth, AE Carpenter, A Bender
– Chemical Research in Toxicology
(2025)
38,
759
Fragment Screening Reveals Novel Scaffolds against Sirtuin-2-Related Protein 1 from Trypanosoma brucei
RA Gomes, M D. Polêto, H Verli, VM Almeida, SR Marana, A Bender, BF Godoi, VTL Rodrigues, F da S. Emery, GHG Trossini
– ACS omega
(2024)
10,
3808
(DOI: 10.1021/acsomega.4c09231)
Author Correction: Cell Painting: a decade of discovery and innovation in cellular imaging.
S Seal, M-A Trapotsi, O Spjuth, S Singh, J Carreras-Puigvert, N Greene, A Bender, AE Carpenter
– Nature Methods
(2024)
22,
447
(DOI: 10.1038/s41592-024-02578-y)
Cell Painting: a decade of discovery and innovation in cellular imaging.
S Seal, M-A Trapotsi, O Spjuth, S Singh, J Carreras-Puigvert, N Greene, A Bender, AE Carpenter
– Nature methods
(2024)
22,
254
(DOI: 10.1038/s41592-024-02528-8)
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
– J Chem Inf Model
(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<i>in vivo</i>and<i>in vitro</i>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<i>in vivo</i>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
– J Cheminform
(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
– J Cheminform
(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)