IMDEA Food – Biostatistics & Bioinformatics Unit

We use Deep Learning methodologies for the modeling and design of drugs and nutraceutics mimicking bioactive compounds (microbial metabolites, food molecules), together with virtual screening and a broad set of Cheminformatics & Computational Chemistry techniques. Our group aims at using experimental and Computational Chemistry-derived data to model structure-activity/property relationships through Machine Learning. Then, using novel generative Deep Learning methodologies, we design new molecules with targeted activities and/or properties.

Recent publications:

1. Colmenarejo, G. “A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit”. J. Chem. Inf. Mod. (2025) Accepted
2. Astigarraga, M.; Sänchez-Ruiz, A.; Diop-Aw, A.; Quintero, R.; Colmenarejo, G. “How Do Microbial Metabolites Interact with their Proteins Targets?” J. Chem. Inf. Mod. (2025). 65, 201−213. DOI: 10.1021/acs.jcim.4c01875
3. Orgaz, C.; Sánchez-Ruiz, A.; Colmenarejo, G. “Identifying and Filling the Chemobiological Gaps of Gut Microbial Metabolites”. J. Chem. Inf. Mod. (2024) 64, 6778-6798. DOI: 10.1021/acs.jcim.4c0090
4. Gil-Pichardo, A.; Sánchez-Ruiz, A.; Colmenarejo, G. «Analysis of Metabolites in Human Gut: Illuminating the Design of Gut-Targeted Drugs» (2023) J. Cheminform. 15, 96. DOI: 10.1186/s13321-023-00768-y
5. Sánchez-Ruiz, A.; Colmenarejo, G. “Systematic Analysis and Prediction of the Target Space of Bioactive Food Compounds: Filling the Chemobiological Gaps» (2022) J. Chem. Inf. & Mod. 62, 3734–3751. DOI: 10.1021/acs.jcim.2c00888
6. Sánchez-Ruiz, A.; Colmenarejo, G. “Updated Prediction of Aggregators and Assay-Interfering Substructures in Food Compounds” (2021) J. Agric. Food Chem. 69, 15184−15194. DOI: 10.1021/acs.jafc.1c05918
7. Kaya, I.; Colmenarejo, G. “Analysis of nuisance substructures and aggregators in a comprehensive database of food chemical compounds” (2020) J Agricultural & Food Chem. 68, 8812–8824. DOI: 1021/acs.jafc.0c02521
8. Colmenarejo, G. Compound Prioritization in Single-Concentration Screening Data Using Ligand Efficiency Indexes (2016) J. Chem. Inf. Mod. 56, 1705–1713. DOI: 10.1021/acs.jcim.6b00299

Research fields:

• Computational chemical biology of food compounds and metabolites
• Molecular design using AI
• Virtual screening (structure- and ligand-based)