Herman van Vlijmen
Professor of Computational drug discovery
- Name
- Prof.dr. H. van Vlijmen
- Telephone
- +31 71 527 3511
- h.van.vlijmen@lacdr.leidenuniv.nl
Professor Van Vlijmen is Professor of Computational Drug Discovery at the Division of Medicinal Chemistry in Leiden.
Professor Van Vlijmen (b. 1965) graduated in 1989 at Leiden University as one of the first students in Bio-Pharmaceutical Sciences. He received his PhD in Physical Chemistry from Harvard University in 1997 on the subject of “Structure, Dynamics, and Thermodynamics of Proteins”.
His PhD research included computational studies on protein loop prediction, protein electrostatics, and normal mode dynamics analysis of proteins withspecial applications to large virus particles. He was a post-doc researcher and an active member of the Harvard University teaching staff up to 2001.
From 1996 to 2005, he worked as a scientist in Computational Drug Discovery at Biogen Idec in Cambridge, MA (USA), on the computational design of small molecules and protein therapeutics. In 2005, he moved to Tibotec Virco (a Johnson & Johnson company) in Mechelen, Belgium, where he is currently Director of Integrative Chem-Bioinformatics.
Prof. Dr. Herman van Vlijmen was appointed as Professor of Computational Drug Discovery at the Division of Medicinal Chemistry in Leiden on April 15th, 2008.
Professor of Computational drug discovery
- Science
- Leiden Academic Centre for Drug Research
- LACDR/Medicinal Chemistry
- Vlachodimou A., Bouma J., Cleyn M. de, Berthelot D., Pype S., Bosmans J.P., Vlijmen H. van, Wroblowski B., Heitman L.H. & IJzerman A.P. (2024), Kinetic profiling of novel spirobenzo-oxazinepiperidinone derivatives as equilibrative nucleoside transporter 1 inhibitors, Purinergic Signalling : .
- Liu X., Ye K., Vlijmen H. van, IJzerman A.P. & Westen G.J.P. van (2023), DrugEx v3: scaffold-constrained drug design with graph transformer-based reinforcement learning, Journal of Cheminformatics 15(1): 24.
- Bongers B.J., Gorostiola González M., Wang X., Vlijmen H. van, Jespers W., Gutiérrez-de-Terán H., Ye K., IJzerman A.P., Heitman L.H. & Westen G.J.P. van (2022), Pan-cancer functional analysis of somatic mutations in G protein-coupled receptors, Scientific Reports 12(1): 21534.
- Liu X., Ye K., Vlijmen H.W.T. van, Emmerich M.T.M., IJzerman A.P. & Westen G.J.P. van (2021), DrugEx v2: de novo design of drug molecules by pareto-based multi-objective reinforcement learning in polypharmacology, Journal of Cheminformatics 13(1): 85.
- Burggraaff L., Vlijmen H.W.T. van., IJzerman A.P. & Westen G.J.P. van (2020), Quantitative prediction of selectivity between the A1 and A2A adenosine receptors, Journal of Cheminformatics 12: 33.
- Burggraaff L. Lenselink E.B. Jespers W. Engelen J. van Bongers B.J. Gorostiola Gonzalez M. Liu R. Hoos H.H. Vlijmen H. van IJzerman A.P. Westen G.J.P. van (2020), Successive statistical and structure-based modeling to identify chemically novel kinase inhibitors, Journal of Chemical Information and Modeling 60(9): 4283-4295.
- Burggraaff L., Veen A. van, Lam C.C., Vlijmen H.W.T., IJzerman A.P. & Westen G.J.P. van (2020), Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs, Journal of Chemical Information and Modeling 60(10): 4664-4672.
- Liu X., Ye K., Vlijmen H.W.T. van, IJzerman A.P. & Westen G.J.P. van (2019), An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A2A receptor, Journal of Cheminformatics 11: 35.
- Sydow D., Burggraaff L., Szengel A., Vlijmen H. van, IJzerman A.P., Westen G.J.P. van & Volkamer A. (2019), Advances and Challenges in Computational Target Prediction, Journal of Chemical Information and Modeling 59(5): 1728-1742.
- Burggraaff L., Oranje P., Gouka R., Pijl P. van der, Geldof M., Vlijmen H.W.T. van, IJzerman A.P. & Westen G.J.P. van (2019), Identification of novel small molecule inhibitors for solute carrier SGLT1 using proteochemometric modeling, Journal of Cheminformatics 11: 15.
- Tresadern G., Trabanco A.A., Pérez-Benito L., Overington J.P., Vlijmen H. van & Westen G.J.P. van (2017), Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling, Journal of Chemical Information and Modeling 57(12): 2976-2985.
- Lenselink E.B., Dijke N. ten, Bongers B.J., Papadatos G., Vlijmen H. van, Kowalczyk W.J., IJzerman A.P. & Westen G.J.P. van (2017), Beyond the Hype: Deep Neural Networks Outperform Established Methods Using A ChEMBL Bioactivity Benchmark Set, Journal of Cheminformatics 9(1): 45.
- Leeuw F.A., Peeters C.F.W., Kester M.I., Harms A.C., Struys E.A., Hankemeier T., Vlijmen H. van, Lee S.J. van der, Duijn C.M. van, Scheltens P., Demirkan A., Wiel M.A. van der, Flier W.M. van der & Teunissen C.E. (2017), Blood-based metabolic signatures in Alzheimer's disease, Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring 8: 196-207.
- Lenselink E.B., Jespers W., Vlijmen H.W.T. van, IJzerman A.P. & Westen G.J.P. van (2016), Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening, Journal of Chemical Information and Modeling 56(10): 2053-2060.
- Lenselink E.B., Louvel J.A., Forti A.F., Veldhoven J.P.D. van, Vries H. de, Mulder-Krieger T., McRobb F.M., Negri A., Goose J., Abel R., Vlijmen H.W.T. van, Wang L., Harder E., Sherman W., IJzerman A.P. & Beuming T. (2016), Predicting binding affinities for GPCR ligands using free-energy perturbation, ACS Omega 1(2): 293-304.
- Costello J.C., Heiser L.M., Georgii E., Gönen M., Menden M.P., Wang N.J., Bansal M., Ammad-ud-din M., Hintsanen P., Khan S.A., Mpindi J-P., Kallioniemi O., Honkela A., Aittokallio T., Wennerberg K., Westen G.J.P van, Lenselink E.B., IJzerman A.P., Vlijmen H.W.T. van, Collins J.J., Gallahan D., Singer D., Saez-Rodriguez J., Kaski S., Gray J.W. & Stolovitzky G. (2014), A community effort to assess and improve drug sensitivity prediction algorithms, Nature Biotechnology 32: 1202–1212.
- Bansal M., Yang J., Karan C ., Menden M.P., Costello J.C., Tang H., Xiao G., Li Y., Allen J., Zhong R., Chen B., Kim M., Wang T., Heiser L.M., Realubit R., Mattioli M., Alvarez M.J., Shen Y., Westen G.J.P. van., IJzerman A.P., Lenselink E.B., Vlijmen H.W.T. van, Wegner J.K., Gallahan D., Singer D., Saez-Rodriguezc J., Xie Y., Stolovitzky G. & Califano A. (2014), A community computational challenge to predict the activity of pairs of compounds, Nature Biotechnology 32: 1213–1222.
- Westen G.J.P. van, Swier R.F., Wegner J.K., IJzerman A.P., Vlijmen H. van & Bender A. (2013), Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets, Journal of Cheminformatics 5: 41.
- Westen G.J.P. van, Hendriks A., Wegner J.K., IJzerman A.P., Vlijmen H.W.T. van & Bender A. (2013), Significantly Improved HIV Inhibitor Efficacy Prediction Employing Proteochemometric Models Generated From Antivirogram, PLoS Computational Biology 9(2): e1002899.
- Sanchez-Faddeev H., Emmerich Michael T.M., Verbeek F.J., Henry A.H., Grimshaw S., Spaink H.P., Vlijmen H.W.T. van & Bender A. (2012), Using multiobjective optimization and energy minimization to design an isoform-selective ligand of the 14-3-3 Protein. Margaria T. & Steffen B. (Eds.), Leveraging applications of formal methods, verification and validation. applications and case studies (ISoLA 2012). International Symposium On Leveraging Applications of Formal Methods, Verification and Validation ISoLA 2012 15 October 2012 - 18 October 2012. Lecture Notes in Computer Science no. 7610. Berlin, Heidelberg: Springer. 12-24.
- Van Westen Gerard J.P., Van den Hoven Olaf O., Van der Pijl Rianne, Mulder-Krieger Thea, De Vries Henk, Wegner Jorg K., Ijzerman Adriaan P., Van Vlijmen Herman W.T. & Bender Andreas (2012), Identifying Novel Adenosine Receptor Ligands by Simultaneous Proteochemometric Modeling of Rat and Human Bioactivity Data, Journal of Medicinal Chemistry 55(16): 7010-7020.
- Van Westen G.J.P., Wegner J.K., IJzerman A.P., Van Vlijmen H.W.T. & Bender A. (2011), Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets, MedChemComm 2(1): 16-30.
- Westen G.J.P. van, Wegner J.K., Geluykens P., Kwanten L., Vereycken I., Peeters A., IJzerman A.P., Vlijmen H. van & Bender A. (2011), Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development, PLoS ONE 6(11): e27518.
- Horst E. van der, Peironcely Julio E., IJzerman A.P., Beukers M.W., Lane J.R., Vlijmen H. van, Emmerich M.T.M., Okuno Yasushi & Bender A. (2010), A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization, BMC Bioinformatics 11: 316.
- Senior Director Molecular Sciences