Data-Driven Drug Discovery and Molecular Informatics

Publications

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  • Currently displaying 41 - 60 of 561 publications
Author(s)
Publication title
Journal Name
Publication year
From Pixels to Phenotypes: Integrating Image-Based Profiling with Cell Health Data Improves Interpretability
S Seal, J Carreras-Puigvert, AE Carpenter, O Spjuth, A Bender
(2023)
(doi: 10.1101/2023.07.14.549031)
Transferable machine learning interatomic potential for bond dissociation energy prediction of drug-like molecule
E Gelžinytė, M Öeren, MD Segall, G Csányi
(2023)
(doi: 10.26434/chemrxiv-2023-l85nf)
wfl Python Toolkit for Creating Machine Learning Interatomic Potentials and Related Atomistic Simulation Workflows
E Gelžinytė, S Wengert, TK Stenczel, HH Heenen, K Reuter, G Csányi, N Bernstein
(2023)
(doi: 10.48550/arxiv.2306.11421)
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
(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
Journal of Medicinal Chemistry
(2023)
66
(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
(doi: 10.1021/acs.molpharmaceut.3c00071)
Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis.
A Bender
BMC Bioinformatics
(2023)
24
(doi: 10.1186/s12859-023-05277-1)
Deep generative models for 3D molecular structure
B Baillif, J Cole, P McCabe, A Bender
Current Opinion in Structural Biology
(2023)
80
(doi: 10.1016/j.sbi.2023.102566)
Mechanism of action deconvolution of the small-molecule pathological tau aggregation inhibitor Anle138b
L Hosseini-Gerami, E Ficulle, N Humphryes-Kirilov, DC Airey, J Scherschel, S Kananathan, BJ Eastwood, S Bose, DA Collier, E Laing, D Evans, H Broughton, A Bender
Alzheimer's Research & Therapy
(2023)
15
(doi: 10.1186/s13195-023-01182-0)
Integrating structure-based approaches in generative molecular design.
M Thomas, A Bender, C de Graaf
Current opinion in structural biology
(2023)
79
(doi: 10.1016/j.sbi.2023.102559)
Analysis of Virtual Control Groups and Inter-species Concordance using Preclinical Toxicity Data
P Wright
(2023)
(doi: 10.17863/CAM.97106)
In silico prediction and biological assessment of novel angiogenesis modulators from traditional Chinese medicine
Y Zhu, H Yang, L Han, LH Mervin, L Hosseini-Gerami, P Li, P Wright, M-A Trapotsi, K Liu, T-P Fan, A Bender
Frontiers in Pharmacology
(2023)
14
(doi: 10.3389/fphar.2023.1116081)
Using chemical and biological data to predict drug toxicity
A Liu, S Seal, H Yang, A Bender
Slas Discovery
(2023)
28
(doi: 10.1016/j.slasd.2022.12.003)
Using Transcriptomics and Cell Morphology Data in Drug Discovery: The Long Road to Practice
L-L Pruteanu, A Bender
ACS MEDICINAL CHEMISTRY LETTERS
(2023)
14
(doi: 10.1021/acsmedchemlett.3c00015)
Prediction of inotropic effect based on calcium transients in human iPSC-derived cardiomyocytes and machine learning.
H Yang, O Obrezanova, A Pointon, W Stebbeds, J Francis, KA Beattie, P Clements, JS Harvey, GF Smith, A Bender
Toxicology and applied pharmacology
(2022)
459
(doi: 10.1016/j.taap.2022.116342)
Statistical analysis of preclinical inter-species concordance of histopathological findings in the eTOX database.
PSR Wright, KA Briggs, R Thomas, GF Smith, G Maglennon, P Mikulskis, M Chapman, N Greene, BU Phillips, A Bender
Regulatory Toxicology and Pharmacology
(2022)
138
(doi: 10.1016/j.yrtph.2022.105308)
Retrospective analysis of the potential use of virtual control groups in preclinical toxicity assessment using the eTOX database
PSR Wright, GF Smith, KA Briggs, R Thomas, G Maglennon, P Mikulskis, M Chapman, N Greene, BU Phillips, A Bender
Regulatory Toxicology and Pharmacology
(2022)
138
(doi: 10.1016/j.yrtph.2022.105309)
Augmented Hill-Climb increases reinforcement learning efficiency for language-based de novo molecule generation.
M Thomas, NM O'Boyle, A Bender, C de Graaf
Journal of Cheminformatics
(2022)
14
(doi: 10.1186/s13321-022-00646-z)
A review of biomedical datasets relating to drug discovery: a knowledge graph perspective.
S Bonner, IP Barrett, C Ye, R Swiers, O Engkvist, A Bender, CT Hoyt, WL Hamilton
Briefings in bioinformatics
(2022)
23
(doi: 10.1093/bib/bbac404)
scRNA-Seq-based drug repurposing targeting idiopathic pulmonary fibrosis (IPF)
A Liu, J-H Lee, N Han, A Bender
(2022)
(doi: 10.1101/2022.09.17.508360)
Yusuf Hamied Department of Chemistry
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