Data-Driven Drug Discovery and Molecular Informatics

Publications

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  • Currently displaying 1 - 20 of 582 publications
Author(s)
Publication title
Journal Name
Publication year
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
(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
(doi: 10.1021/acs.chemrestox.5c00033)
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
(doi: 10.1021/acsomega.4c09231)
Correction to: Cell Painting: a decade of discovery and innovation in cellular imaging (Nature Methods, (2025), 22, 2, (254-268), 10.1038/s41592-024-02528-8)
S Seal, M-A Trapotsi, O Spjuth, S Singh, J Carreras-Puigvert, N Greene, A Bender, AE Carpenter
Nature methods
(2024)
22
(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
Nat Methods
(2024)
22
(doi: 10.1038/s41592-024-02528-8)
Improving ligand discovery using deep learning on three-dimensional structural data
B Baillif
(2024)
(doi: 10.17863/CAM.119823)
Graph neural processes for molecules: an evaluation on docking scores and strategies to improve generalization
M García-Ortegón, S Seal, C Rasmussen, A Bender, S Bacallado
J Cheminform
(2024)
16
(doi: 10.1186/s13321-024-00904-2)
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
(doi: 10.1021/acs.jcim.4c01314)
Learning Molecular Representation in a Cell.
G Liu, S Seal, J Arevalo, Z Liang, AE Carpenter, M Jiang, S Singh
(2024)
Modelling fitness and stability of G protein-coupled receptor variants
A Boardman
(2024)
(doi: 10.17863/CAM.115724)
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
(doi: 10.1021/acs.jcim.4c00921)
Using Cell Painting and Chemical Data for Small-molecule Bioactivity and Toxicity Prediction
S Seal
(2024)
(doi: 10.17863/CAM.113032)
Improved Detection of Drug-Induced Liver Injury by Integrating Predicted In Vivo and In Vitro Data
S Seal, D Williams, L Hosseini-Gerami, M Mahale, AE Carpenter, O Spjuth, A Bender
Chem Res Toxicol
(2024)
37
(doi: 10.1021/acs.chemrestox.4c00015)
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)
Learning Molecular Representation in a Cell
G Liu, S Seal, J Arevalo, Z Liang, AE Carpenter, M Jiang, S Singh
(2024)
(doi: 10.48550/arxiv.2406.12056)
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)
MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design
M Thomas, NM O'Boyle, A Bender, C De Graaf
J Cheminform
(2024)
16
(doi: 10.1186/s13321-024-00861-w)
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)
Yusuf Hamied Department of Chemistry
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