Presented The first OpenBind release as a poster and flash presentation at the 10th RSC-BMCS Fragment-based Drug Discovery Meeting in Cambridge. Poster ↗
Computational chemist · University of Oxford
Jochem Nelen
Postdoctoral Research Associate · Oxford Protein Informatics Group
I develop and evaluate computational methods for structure-based drug discovery, with a focus on protein-ligand modelling, virtual screening, benchmarking, and experimentally grounded datasets.
About
Research at the interface of computation and drug discovery
I am currently working as a Postdoctoral Research Associate in the Oxford Protein Informatics Group (OPIG) at the University of Oxford. Within OpenBind, my research focuses on protein-ligand binding prediction, benchmark development, and the curation and analysis of large-scale structural and affinity datasets.
During my PhD at UCAM, completed summa cum laude, I developed consensus-based virtual screening methods and applied them to hit identification and lead optimisation projects in collaboration with academic and industrial partners.
I am particularly interested in making virtual screening more reliable across each stage of the workflow, from receptor selection and pose generation to rescoring, consensus ranking, and hit prioritisation. A central goal is to improve enrichment and hit rates by understanding where current workflows fail and by integrating complementary computational and experimental information.
Recent work
Recent research and outputs
The first OpenBind structure-affinity dataset and benchmark for structure-based AI is now available as a preprint. Preprint ↗
Our work on WEE1-targeting inhibitors, from virtual screening to lead discovery, published in Bioorganic & Medicinal Chemistry. Paper ↗
Published our computational discovery and optimisation study of a potent, selective p38α inhibitor scaffold. Paper ↗
Publications
2026
STELLAR: A Fragment-Based Docking Workflow for Highly Flexible Long-Chain Biopolymers
Journal of Chemical Information and Modeling. ASAP article.
Paper ↗2026
Freshness flavour perception via quantum-inspired and quantum ligand-based virtual screening
Scientific Reports.
Paper ↗2026
Preprint
The first OpenBind release: An open experimental structure-affinity dataset and benchmark for structure-based AI
bioRxiv.
Preprint ↗ Poster ↗2026
Wee1-targeting inhibitors: From virtual screening to lead discovery
Bioorganic & Medicinal Chemistry 138, 118645.
Paper ↗2026
Computational Discovery and Optimization of a Potent, Selective, and Drug-Like Scaffold for p38α Inhibition
Drug Design, Development and Therapy 20, 585325.
Paper ↗2026
Discovery of Novel Molecular Scaffolds to Overcome Pseudomonas aeruginosa Aminoglycoside Resistance: Insights for a Consensus Scoring Rational Design Approach
International Journal of Molecular Sciences 27(6), 2642.
Paper ↗2026
Enhancing Drug Repurposing with Consensus Docking: Discovery of Novel Discoidin Domain Receptor 1 Inhibitors
ChemMedChem 21(2), e202500747.
Paper ↗2025
Targeting drug resistance in cancer: Dimethoxycurcumin as a functional antioxidant targeting ABCC3
Antioxidants 14(5), 599.
Paper ↗2025
Matched pairs demonstrate robustness against inter-assay variability
Journal of Cheminformatics 17, 8.
Paper ↗2024
Interaction of anticancer oxygenated propenylbenzene derivatives with human topoisomerase IIα and actin: molecular modeling and isothermal titration calorimetry studies
Journal of Thermal Analysis and Calorimetry.
Paper ↗2024
Enhancing MD simulations: ASGARD's automated analysis for GROMACS
Journal of Biomolecular Structure and Dynamics.
Paper ↗2024
2023
Antcin-B, a phytosterol-like compound from Taiwanofungus camphoratus, inhibits SARS-CoV-2 3-chymotrypsin-like protease activity in silico and in vitro
Scientific Reports 13, 17106.
Paper ↗2020
Identifying isoniazid resistance markers to guide inclusion of high-dose isoniazid in tuberculosis treatment regimens
Clinical Microbiology and Infection 26(10), 1332-1337.
Paper ↗Posters & talks
Selected conference contributions
Poster PDFs are available directly from the previews below.
Postdoctoral Research Associate
Oxford Protein Informatics Group, University of Oxford
OpenBind research on protein-ligand binding prediction, benchmark design, docking, and co-folding, contributing to high-quality experimental datasets for the next generation of AI models for structure-based drug discovery.
PhD in Health Sciences
BIO-HPC, UCAM Universidad Católica San Antonio de Murcia
Consensus-based virtual screening methods and computational-experimental drug-discovery projects. Summa cum laude.
Visiting Research Intern
McCarthy Team, EMBL Grenoble
Fragment-informed virtual screening and structure-guided pharmacophore modelling, including exploration of fragment linking with DiffLinker.
Visiting Research Intern
UAMC, University of Antwerp
Inter-assay variability in ChEMBL bioactivity data, including work in collaboration with Drug Discovery Data Sciences at Janssen Pharmaceutica NV.
MSc Biochemistry and Biotechnology
University of Antwerp
Master's thesis carried out at UAMC under the supervision of Prof. Hans De Winter, developing a user-friendly web tool for displaying free-energy perturbation calculations.
BSc Biochemistry and Biotechnology
University of Antwerp
Bachelor's thesis carried out at BIOMINA under the supervision of Prof. Kris Laukens, investigating resistance markers for isoniazid in Mycobacterium tuberculosis. This work contributed to a subsequent publication in Clinical Microbiology and Infection ↗.
Contact
Get in touch
For research discussions, collaborations, or questions about my work, feel free to contact me.