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Data-Driven Drug Discovery and Molecular Informatics

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  • Currently displaying 1 - 20 of 572 publications
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,
115
(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,
7905
(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)
(link to publication)
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)
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
– Chemical research in toxicology
(2024)
37,
1290
(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 Predictedin vivoandin vitroData
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,
64
(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
(2024)
(doi: 10.48550/arxiv.2405.02767)
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)
(link to publication)
PromptSMILES: Prompting for scaffold decoration and fragment linking in chemical language models
M Thomas, M Ahmad, G Tresadern, G de Fabritiis
(2024)
(doi: 10.26434/chemrxiv-2024-z5jnt)
MolScore: A scoring and evaluation framework for de novo drug design
M Thomas, NM O'Boyle, A Bender, C de Graaf
(2024)
(doi: 10.26434/chemrxiv-2023-c4867)
PKSmart: An Open-Source Computational Model to Predictin vivoPharmacokinetics 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 DICTrank
S Seal, O Spjuth, L Hosseini-Gerami, M García-Ortegón, S Singh, A Bender, AE Carpenter
– Journal of Chemical Information and Modeling
(2024)
64,
1172
(doi: 10.1021/acs.jcim.3c01834)
Using Generative Modeling to Endow with Potency Initially Inert Compounds with Good Bioavailability and Low Toxicity
RI Horne, J Wilson-Godber, A González Díaz, ZF Brotzakis, S Seal, RC Gregory, A Possenti, S Chia, M Vendruscolo
– J Chem Inf Model
(2024)
64,
590
(doi: 10.1021/acs.jcim.3c01777)
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)

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