Denis Fourches

A critical overview of computational approaches employed for COVID-19 drug discovery

Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., … Tropsha, A. (2021, July 2). CHEMICAL SOCIETY REVIEWS.

CATMoS: Collaborative Acute Toxicity Modeling Suite

ENVIRONMENTAL HEALTH PERSPECTIVES, 129(4).

Cheminformatics Analysis of Fluoroquinolones and Their Inhibition Potency Against Four Pathogens

MOLECULAR INFORMATICS, 40(5).

SMILES Pair Encoding: A Data-Driven Substructure Tokenization Algorithm for Deep Learning

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 61(4), 1560–1569.

The VKORC1 ER-luminal loop mutation (Leu76Pro) leads to a significant resistance to warfarin in black rats (Rattus rattus)

PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY, 173.

Benchmarking 2D/3D/MD-QSAR Models for Imatinib Derivatives: How Far Can We Predict?

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 60(7), 3342–3360.

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

ENVIRONMENTAL HEALTH PERSPECTIVES, 128(2).

Hierarchical Quantitative Structure-Activity Relationship Modeling Approach for Integrating Binary, Multiclass, and Regression Models of Acute Oral Systemic Toxicity

CHEMICAL RESEARCH IN TOXICOLOGY, 33(2), 353–366.

INTEGRATIVE STATISTICAL METHODS FOR EXPOSURE MIXTURES AND HEALTH

ANNALS OF APPLIED STATISTICS, 14(4), 1945–1963.

In vitroandin vivoEvaluation ofin silicoPredicted Pneumococcal UDPG:PP Inhibitors

FRONTIERS IN MICROBIOLOGY, 11.

Inductive transfer learning for molecular activity prediction: Next-Gen QSAR Models with MolPMoFiT

JOURNAL OF CHEMINFORMATICS, 12(1).

Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities

JOURNAL OF CHROMATOGRAPHY A, 1625.

Photoinduced reconfiguration to control the protein-binding affinity of azobenzene-cyclized peptides

JOURNAL OF MATERIALS CHEMISTRY B, 8(33), 7413–7427.

QSAR without borders

[Review of ]. CHEMICAL SOCIETY REVIEWS, 49(11), 3525–3564.

QSAR without borders (vol 10, pg 531, 2020)

Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., … Tropsha, A. (2020, June 7). CHEMICAL SOCIETY REVIEWS, Vol. 49, pp. 3716–3716.

SIME: synthetic insight-based macrolide enumerator to generate the V1B library of 1 billion macrolides

Journal of Cheminformatics, 12(1).

Structural-based connectivity and omic phenotype evaluations (SCOPE): a cheminformatics toolbox for investigating lipidomic changes in complex systems

ANALYST, 145(22), 7197–7209.

Structure-based virtual screening of perfluoroalkyl and polyfluoroalkyl substances (PFASs) as endocrine disruptors of androgen receptor activity using molecular docking and machine learning

ENVIRONMENTAL RESEARCH, 190.

Unveiling molecular signatures of preeclampsia and gestational diabetes mellitus with multi-omics and innovative cheminformatics visualization tools

MOLECULAR OMICS, 16(6).

4D-quantitative structure-activity relationship modeling: making a comeback

[Review of ]. EXPERT OPINION ON DRUG DISCOVERY, 14(12), 1227–1235.

Adipocytes as Anticancer Drug Delivery Depot

MATTER, 1(5), 1203–1214.

Binding of peanut allergen Ara h 2 with Vaccinium fruit polyphenols

FOOD CHEMISTRY, 284, 287–295.

Cheminformatics approach to exploring and modeling trait-associated metabolite profiles

JOURNAL OF CHEMINFORMATICS, 11.

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

NATURE COMMUNICATIONS, 10.

Corrections to “Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library”

Corrections to “Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library.” ACS Sustainable Chemistry & Engineering, 7(1), 1806–1806.

Identifying individual risk rare variants using protein structure guided local tests (POINT)

PLOS COMPUTATIONAL BIOLOGY, 15(2).

Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples

[Review of ]. TRAC-TRENDS IN ANALYTICAL CHEMISTRY, 116, 292–299.

Student-Guided Three-Dimensional Printing Activity in Large Lecture Courses: A Practical Guideline

JOURNAL OF CHEMICAL EDUCATION, 96(2), 291–295.

Adverse drug reactions triggered by the common HLA-B*57:01 variant: Virtual screening of DrugBank using 3D molecular docking

Journal of Cheminformatics, 10.

Cheminformatics Analysis of Dynamic WNK-Inhibitor Interactions

Molecular Informatics, 37(6-7), 1700138.

Cheminformatics-based enumeration and analysis of large libraries of macrolide scaffolds

Journal of Cheminformatics, 10(1).

Chemistry-Wide Association Studies (CWAS): A Novel Framework for Identifying and Interpreting Structure-Activity Relationships

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 58(11), 2203–2213.

Confirmation of high-throughput screening data and novel mechanistic insights into VDR-xenobiotic interactions by orthogonal assays

Scientific Reports, 8(1).

Exploring drug space with ChemMaps.com

BIOINFORMATICS, 34(21), 3773–3775.

In silico Predicted Glucose-1-phosphate Uridylyltransferase (GalU) Inhibitors Block a Key Pathway Required for Listeria Virulence

Molecular Informatics, 37(6-7), 1800004.

Janus kinase inhibitors differ in their affinity to the TRPV1 receptor - implications for their use in itch and pain

Journal of Veterinary Pharmacology and Therapeutics, 41, 160–160.

Predicting Adverse Drug Effects from Literature- and Database-Mined Assertions

DRUG SAFETY, 41(11), 1059–1072.

Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 1. Database Development and Analysis

ACS SUSTAINABLE CHEMISTRY & ENGINEERING, 6(2), 2344–2352.

Toward the Rational Design of Sustainable Hair Dyes Using Cheminformatics Approaches: Step 2. Identification of Hair Dye Substance Database Analogs in the Max Weaver Dye Library

ACS SUSTAINABLE CHEMISTRY & ENGINEERING, 6(11), 14248–14256.

Adverse drug reactions triggered by the common HLA-B*57:01 variant: A molecular docking study

Journal of Cheminformatics, 9.

Characterizing the Chemical Space of ERK2 Kinase Inhibitors Using Descriptors Computed from Molecular Dynamics Trajectories

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 57(6), 1286–1299.

Cheminformatics Modeling of Amine Solutions for Assessing their CO2Absorption Properties

Molecular Informatics, 36(7), 1600143.

Cheminformatics modeling of amine solutions for assessing their CO2 absorption properties

Molecular Informatics, 36(7).

Computer-assisted decision support for student admissions based on their predicted academic performance

American Journal of Pharmaceutical Education, 81(3).

Genome-wide common and rare variant analysis provides novel insights into clozapine-associated neutropenia

Molecular Psychiatry, 22(10), 1502–1508.

Reaction: Molecular Modeling for Novel Antibacterials

Chem, 3(1), 13–14.

RealityConvert: a tool for preparing 3D models of biochemical structures for augmented and virtual reality

BIOINFORMATICS, 33(23), 3816–3818.

Weaver's historic accessible collection of synthetic dyes: a cheminformatics analysis

CHEMICAL SCIENCE, 8(6), 4334–4339.

Activity prediction and identification of mis-annotated chemical compounds using extreme descriptors

Journal of Chemometrics, 30(3), 99–108.

Alarms about structural alerts

GREEN CHEMISTRY, 18(16), 4348–4360.

Comprehensive characterization of the Published Kinase Inhibitor Set

Nature Biotechnology, 34(1), 95–103.

Computer-aided design of carbon nanotubes with the desired bioactivity and safety profiles

NANOTOXICOLOGY, 10(3), 374–383.

QSAR Modeling and Prediction of Drug-Drug Interactions

MOLECULAR PHARMACEUTICS, 13(2), 545–556.

QSAR models of human data can enrich or replace LLNA testing for human skin sensitization

GREEN CHEMISTRY, 18(24), 6501–6515.

Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56(7), 1243–1252.

Comprehensive characterization of the Published Kinase Inhibitor Set

Nature Biotechnology, 34(1), 95–103.

Curation of chemogenomics data

Fourches, D., Muratov, E., & Tropsha, A. (2015, August).

Drug Side Effect Profiles as Molecular Descriptors for Predictive Modeling of Target Bioactivity

Molecular Informatics, 34(2-3), 160–170.

Materials Cartography: Representing and Mining Materials Space Using Structural and Electronic Fingerprints

Chemistry of Materials, 27(3), 735–743.

Pred-hERG: A Novel web-Accessible Computational Tool for Predicting Cardiac Toxicity

MOLECULAR INFORMATICS, 34(10), 698–701.

Predicting chemically-induced skin reactions. Part I: QSAR models of skin sensitization and their application to identify potentially hazardous compounds

Toxicology and Applied Pharmacology, 284(2), 262–272.

Predicting chemically-induced skin reactions. Part II: QSAR models of skin permeability and the relationships between skin permeability and skin sensitization

Toxicology and Applied Pharmacology, 284(2), 273–280.

Chemical Basis of Interactions Between Engineered Nanoparticles and Biological Systems

Chemical Reviews, 114(15), 7740–7781.

Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles

Nature Communications, 5(1).

Data Set Modelability by QSAR

Journal of Chemical Information and Modeling, 54(1), 1–4.

Expanding the scope of drug repurposing in pediatrics: The Children's Pharmacy Collaborative™

Drug Discovery Today, 19(11), 1696–1698.

QSAR Modeling: Where Have You Been? Where Are You Going To?

Journal of Medicinal Chemistry, 57(12), 4977–5010.

Discovery of Novel Antimalarial Compounds Enabled by QSAR-Based Virtual Screening

Journal of Chemical Information and Modeling, 53(2), 475–492.

Integrative Chemical–Biological Read-Across Approach for Chemical Hazard Classification

Chemical Research in Toxicology, 26(8), 1199–1208.

Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches

Journal of Chemical Information and Modeling, 53(8), 1915–1922.

Using Graph Indices for the Analysis and Comparison of Chemical Datasets

Molecular Informatics, 32(9-10), 827–842.

Human Intestinal Transporter Database: QSAR Modeling and Virtual Profiling of Drug Uptake, Efflux and Interactions

Pharmaceutical Research, 30(4), 996–1007.

Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches

Chemical Research in Toxicology, 24(8), 1251–1262.

Applicability Domains for Classification Problems: Benchmarking of Distance to Models for Ames Mutagenicity Set

Journal of Chemical Information and Modeling, 50(12), 2094–2111.

Cheminformatics Analysis of Assertions Mined from Literature That Describe Drug-Induced Liver Injury in Different Species

Chemical Research in Toxicology, 23(1), 171–183.

Modeling Liver-Related Adverse Effects of Drugs UsingkNearest Neighbor Quantitative Structure−Activity Relationship Method

Chemical Research in Toxicology, 23(4), 724–732.

Quantitative Nanostructure−Activity Relationship Modeling

ACS Nano, 4(10), 5703–5712.

Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research

Journal of Chemical Information and Modeling, 50(7), 1189–1204.

Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis

Journal of Chemical Information and Modeling, 48(4), 766–784.

Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection

Journal of Chemical Information and Modeling, 48(9), 1733–1746.

QSPR Modeling of the AmIII/EuIIISeparation Factor: How Far Can we Predict ?

Solvent Extraction and Ion Exchange, 25(1), 1–26.

Successful “In Silico” Design of New Efficient Uranyl Binders

Solvent Extraction and Ion Exchange, 25(4), 433–462.

Benchmarking of Linear and Nonlinear Approaches for Quantitative Structure−Property Relationship Studies of Metal Complexation with Ionophores

Journal of Chemical Information and Modeling, 46(2), 808–819.

Substructural fragments: an universal language to encode reactions, molecular and supramolecular structures

Journal of Computer-Aided Molecular Design, 19(9-10), 693–703.

“In Silico” Design of New Uranyl Extractants Based on Phosphoryl-Containing Podands:  QSPR Studies, Generation and Screening of Virtual Combinatorial Library, and Experimental Tests

Journal of Chemical Information and Computer Sciences, 44(4), 1365–1382.