H
Herman W. T. van Vlijmen
Researcher at Leiden University
Publications - 67
Citations - 2603
Herman W. T. van Vlijmen is an academic researcher from Leiden University. The author has contributed to research in topics: Medicine & Virtual screening. The author has an hindex of 29, co-authored 60 publications receiving 2351 citations. Previous affiliations of Herman W. T. van Vlijmen include Biogen Idec & Johnson & Johnson.
Papers
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Journal ArticleDOI
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set
Eelke B. Lenselink,Niels ten Dijke,Brandon J. Bongers,George Papadatos,George Papadatos,Herman W. T. van Vlijmen,Wojtek Kowalczyk,Adriaan P. IJzerman,Gerard J. P. van Westen +8 more
TL;DR: A standardized set to test and evaluate different machine learning algorithms in the context of multi-task learning is offered by providing the data and the protocols.
Journal ArticleDOI
Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design
Louis A. Clark,P. Ann Boriack-Sjodin,John Eldredge,Christopher Fitch,Bethany Friedman,Karl J. M. Hanf,Matthew Jarpe,Stefano F. Liparoto,You Li,Alexey Lugovskoy,Miller Stephan S,Mia Rushe,Woody Sherman,Kenneth Simon,Herman W. T. van Vlijmen +14 more
TL;DR: The results indicate that structure‐based computational design can be successfully applied to further improve the binding of high‐affinity antibodies and improve the single‐mutant success rate.
Journal ArticleDOI
Improving the accuracy of protein pKa calculations: Conformational averaging versus the average structure
TL;DR: It is suggested that the observed improvement of pKa values in the present studies is due not to averaging over an ensemble of structures, but rather to the generation of a single properly averaged structure for the pKa calculation.
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Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets
Gerard J. P. van Westen,Jörg K. Wegner,Adriaan P. IJzerman,Herman W. T. van Vlijmen,Andreas Bender +4 more
TL;DR: It is concluded that proteochemometrics is a promising technique in preclinical drug research that allows merging data sets that were previously considered separately, with the potential to extrapolate more reliably both in ligand as well as target space.
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Identification of a new murine tumor necrosis factor receptor locus that contains two novel murine receptors for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL).
Pascal Schneider,Dian L. Olson,Aubry Tardivel,Beth Browning,Alexey Lugovskoy,Dahai Gong,Max Dobles,Sylvie Hertig,Kay Hofmann,Herman W. T. van Vlijmen,Yen-Ming Hsu,Linda C. Burkly,Jürg Tschopp,Timothy S. Zheng +13 more
TL;DR: In this article, the authors identified a murine chromosomal locus that contains three new TNF receptor-related genes, mDcTrailr1 and -r2, which encode the first described murine decoy receptors for TRAIL.