Herman van Vlijmen
Herman van Vlijmen
Head, Computational Chemistry
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Evaluation of comparative protein modeling by MODELLER
A Šali, L Potterton, F Yuan, H van Vlijmen, M Karplus
Proteins: structure, function, and bioinformatics 23 (3), 318-326, 1995
A community effort to assess and improve drug sensitivity prediction algorithms
JC Costello, LM Heiser, E Georgii, M Gönen, MP Menden, NJ Wang, ...
Nature biotechnology 32 (12), 1202-1212, 2014
Normal mode analysis: theory and applications to biological and chemical systems
Q Cui, I Bahar
CRC press, 2005
A community computational challenge to predict the activity of pairs of compounds
M Bansal, J Yang, C Karan, MP Menden, JC Costello, H Tang, G Xiao, ...
Nature biotechnology 32 (12), 1213-1222, 2014
Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set
EB Lenselink, N Ten Dijke, B Bongers, G Papadatos, HWT Van Vlijmen, ...
Journal of cheminformatics 9, 1-14, 2017
Affinity enhancement of an in vivo matured therapeutic antibody using structure‐based computational design
LA Clark, PA Boriack‐Sjodin, J Eldredge, C Fitch, B Friedman, KJM Hanf, ...
Protein science 15 (5), 949-960, 2006
PDB-based protein loop prediction: parameters for selection and methods for optimization
HWT van Vlijmen, M Karplus
Journal of molecular biology 267 (4), 975-1001, 1997
Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure
HWT van Vlijmen, M Schaefer, M Karplus
Proteins: Structure, Function, and Bioinformatics 33 (2), 145-158, 1998
Proteochemometric modeling as a tool to design selective compounds and for extrapolating to novel targets
GJP Van Westen, JK Wegner, AP IJzerman, HWT Van Vlijmen, A Bender
MedChemComm 2 (1), 16-30, 2011
Large scale relative protein ligand binding affinities using non-equilibrium alchemy
V Gapsys, L Pérez-Benito, M Aldeghi, D Seeliger, H Van Vlijmen, ...
Chemical Science 11 (4), 1140-1152, 2020
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)
P Schneider, D Olson, A Tardivel, B Browning, A Lugovskoy, DH Gong, ...
Journal of Biological Chemistry 278 (7), 5444-5454, 2003
Trends in antibody sequence changes during the somatic hypermutation process
LA Clark, S Ganesan, S Papp, HWT van Vlijmen
The Journal of Immunology 177 (1), 333-340, 2006
Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets
GJP van Westen, RF Swier, JK Wegner, AP IJzerman, HWT van Vlijmen, ...
Journal of cheminformatics 5, 1-11, 2013
Predicting binding affinities for GPCR ligands using free-energy perturbation
EB Lenselink, J Louvel, AF Forti, JPD van Veldhoven, H de Vries, ...
ACS omega 1 (2), 293-304, 2016
Mutations of the anti-mullerian hormone gene in patients with persistent mullerian duct syndrome: biosynthesis, secretion, and processing of the abnormal proteins and analysis …
C Belville, H Van Vlijmen, C Ehrenfels, B Pepinsky, AR Rezaie, JY Picard, ...
Molecular Endocrinology 18 (3), 708-721, 2004
Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein
D Roymans, HL De Bondt, E Arnoult, P Geluykens, T Gevers, ...
Proceedings of the National Academy of Sciences 107 (1), 308-313, 2010
Advances and challenges in computational target prediction
D Sydow, L Burggraaff, A Szengel, HWT van Vlijmen, AP IJzerman, ...
Journal of chemical information and modeling 59 (5), 1728-1742, 2019
The role of polar interactions in the molecular recognition of CD40L with its receptor CD40
J Singh, E Garber, HV Vlijmen, M Karpusas, YM Hsu, Z Zheng, D Thomas, ...
Protein science 7 (5), 1124-1135, 1998
Electrostatic contributions to molecular free energies in solution
M Schaefer, HWT Van Vlijmen, M Karplus
Advances in protein chemistry 51, 1-58, 1998
Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets
GJP van Westen, RF Swier, I Cortes-Ciriano, JK Wegner, JP Overington, ...
Journal of cheminformatics 5, 1-20, 2013
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