Denis Fourches

Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes

Wu, T., Yu, J. C., Suresh, A., Gale-Day, Z. J., Alteen, M. G., Woo, A. S., … Gestwicki, J. E. (2024, May 14). Nature Biotechnology, Vol. 5.

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, January 1). Chemical Society Reviews.

CATMoS: Collaborative Acute Toxicity Modeling Suite

Mansouri, K., Karmaus, A. L., Fitzpatrick, J., Patlewicz, G., Pradeep, P., Alberga, D., … Zorn, K. M. (2021, April 1). Environmental Health Perspectives.

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

Li, X., & Fourches, D. (2021, March 15). Journal of Chemical Information and Modeling.

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

Takeda, K., Ikenaka, Y., Fourches, D., Tanaka, K. D., Nakayama, S. M. M., Triki, D., … Ishizuka, M. (2021, January 10). Pesticide Biochemistry and Physiology.

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

Zin, P. P. K., Borrel, A., & Fourches, D. (2020, July 5). Journal of Chemical Information and Modeling, Vol. 60, pp. 3342–3360.

Cheminformatics Analysis of Fluoroquinolones and their Inhibition Potency Against Four Pathogens

Borrel, A., Melander, C., & Fourches, D. (2020, November 30). Molecular Informatics.

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

Mansouri, K., Kleinstreuer, N., Abdelaziz, A. M., Alberga, D., Alves, V. M., Andersson, P. L., … Judson, R. S. (2020, February 1). Environmental Health Perspectives.

Correction: QSAR without borders

Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., … Tropsha, A. (2020, January 1). Chemical Society Reviews.

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

Li, X., Kleinstreuer, N. C., & Fourches, D. (2020, January 24). Chemical Research in Toxicology.

In vitro and in vivo Evaluation of in silico Predicted Pneumococcal UDPG:PP Inhibitors

Cools, F., Triki, D., Geerts, N., Delputte, P., Fourches, D., & Cos, P. (2020, July 15). Frontiers in Microbiology.

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

Li, X., & Fourches, D. (2020, April 22). Journal of Cheminformatics.

Integrative statistical methods for exposure mixtures and health

Reich, B. J., Guan, Y., Fourches, D., Warren, J. L., Sarnat, S. E., & Chang, H. H. (2020, December 1). The Annals of Applied Statistics, Vol. 14, pp. 1945–1963.

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

Reese, H. R., Xiao, X., Shanahan, C. C., Chu, W., Driessche, G. A. V. D., Fourches, D., … Menegatti, S. (2020, May 23). Journal of Chromatography A, Vol. 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

Muratov, E. N., Bajorath, J., Sheridan, R. P., Tetko, I. V., Filimonov, D., Poroikov, V., … Tropsha, A. (2020, January 1). Chemical Society Reviews.

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

Odenkirk, M. T., Zin, P. P. K., Ash, J. R., Reif, D. M., Fourches, D., & Baker, E. S. (2020, January 1). The Analyst, Vol. 145, pp. 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

Singam, E. R. A., Tachachartvanich, P., Fourches, D., Soshilov, A., Hsieh, J. C. Y., Merrill, M. A. L., … Durkin, K. A. (2020, July 28). Environmental Research.

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

Odenkirk, M. T., Stratton, K. G., Gritsenko, M. A., Bramer, L. M., Webb-Robertson, B.-J. M., Bloodsworth, K. J., … Baker, E. S. (2020, September 8). Molecular Omics, Vol. 16.

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

Fourches, D., & Ash, J. (2019, September 12). Expert Opinion on Drug Discovery.

Adipocytes as Anticancer Drug Delivery Depot

Wen, D., Wang, J., Driessche, G. V. D., Chen, Q., Zhang, Y., Chen, G., … Gu, Z. (2019, September 25). Matter.

Binding of peanut allergen Ara h 2 with Vaccinium fruit polyphenols

Plundrich, N. J., Cook, B. T., Maleki, S. J., Fourches, D., & Lila, M. A. (2019, January 18). Food Chemistry, Vol. 284, pp. 287–295.

Cheminformatics approach to exploring and modeling trait-associated metabolite profiles

Ash, J. R., Kuenemann, M. A., Rotroff, D., Motsinger-Reif, A., & Fourches, D. (2019, June 24). Journal of Cheminformatics.

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

Menden, M. P., Wang, D., Mason, M. J., Szalai, B., Bulusu, K. C., Guan, Y., … Fourches, D. (2019, June 17). Nature Communications.

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

West, R. M., Lu, W., Rotroff, D. M., Kuenemann, M. A., Chang, S.-M., Wu, M. C., … Tzeng, J.-Y. (2019, February 19). PLoS Computational Biology, Vol. 15.

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

Burnum-Johnson, K. E., Zheng, X., Dodds, J. N., Ash, J., Fourches, D., Nicora, C. D., … Baker, E. S. (2019, April 29). TrAC Trends in Analytical Chemistry, Vol. 116, pp. 292–299.

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

Low, Y. S., Alves, V. M., Fourches, D., Sedykh, A., Andrade, C. H., Muratov, E. N., … Tropsha, A. (2018, October 30). Journal of Chemical Information and Modeling.

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

Scientific Reports, 8(1).

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.

Exploring drug space with ChemMaps.com

Borrel, A., Kleinstreuer, N. C., & Fourches, D. (2018, May 18). Bioinformatics.

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

La, M. K., Sedykh, A., Fourches, D., Muratov, E., & Tropsha, A. (2018, June 6). Drug Safety.

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

Fourches, D., & Feducia, J. (2018, December 31). Journal of Chemical Education, Vol. 96, pp. 291–295.

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

Williams, T. N., Driessche, G. A. V. D., Valery, A. R. B., Fourches, D., & Freeman, H. S. (2018, September 26). ACS Sustainable Chemistry & Engineering, Vol. 6, pp. 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

Ash, J., & Fourches, D. (2017, May 4). Journal of Chemical Information and Modeling.

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).

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

Borrel, A., & Fourches, D. (2017, August 1). Bioinformatics.

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

Williams, T. N., Kuenemann, M. A., Driessche, G. A. V. D., Williams, A. J., Fourches, D., & Freeman, H. S. (2017, December 22). ACS Sustainable Chemistry & Engineering, Vol. 6, pp. 2344–2352.

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

Kuenemann, M. A., Szymczyk, M., Chen, Y., Sultana, N., Hinks, D., Freeman, H. S., … Vinueza, N. R. (2017, January 1). Chemical Science, Vol. 8, pp. 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

Alves, V. M., Muratov, E. N., Capuzzi, S. J., Politi, R., Low, Y., Braga, R. C., … Tropsha, A. (2016, January 1). Green Chemistry.

Comprehensive characterization of the Published Kinase Inhibitor Set

Nature Biotechnology, 34(1), 95–103.

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

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

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

Alves, V. M., Capuzzi, S. J., Muratov, E. N., Braga, R. C., Thornton, T. E., Fourches, D., … Tropsha, A. (2016, January 1). Green Chemistry.

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

Fourches, D., Muratov, E., & Tropsha, A. (2016, June 9). Journal of Chemical Information and Modeling.

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

Fourches, D., Pu, D., Li, L., Zhou, H., Mu, Q., Su, G., … Tropsha, A. (2015, November 2). Nanotoxicology.

Curation of chemogenomics data

Fourches, D., Muratov, E., & Tropsha, A. (2015, July 21). Nature Chemical Biology.

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

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

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.

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

Braga, R. C., Alves, V. M., Silva, M. F. B., Muratov, E., Fourches, D., Lião, L. M., … Andrade, C. H. (2015, July 20). Molecular Informatics.

QSAR Modeling and Prediction of Drug–Drug Interactions

Zakharov, A. V., Varlamova, E. V., Lagunin, A. A., Dmitriev, A. V., Muratov, E. N., Fourches, D., … Nicklaus, M. C. (2015, December 15). Molecular Pharmaceutics.

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).

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

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

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

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

Data Set Modelability by QSAR

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

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.

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

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