| 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 | 1374 | 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 | 790 | 2014 |
| Normal mode analysis: theory and applications to biological and chemical systems Q Cui, I Bahar CRC press, 2005 | 437 | 2005 |
| 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 | 330 | 2017 |
| 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 | 328 | 2014 |
| 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 | 221 | 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 | 216 | 1997 |
| 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 | 204 | 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 | 203 | 2020 |
| 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 | 201 | 1998 |
| 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 | 165 | 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 | 137 | 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 | 135 | 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 | 130 | 2016 |
| 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 | 116 | 2019 |
| 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 | 116 | 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 | 105 | 2010 |
| 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 | 101 | 2013 |
| 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 | 98 | 1998 |
| Electrostatic contributions to molecular free energies in solution M Schaefer, HWT Van Vlijmen, M Karplus Advances in protein chemistry 51, 1-58, 1998 | 94 | 1998 |
Prof. Gerard JP van WestenPI Computational Drug Discovery (Professor AI & Med Chem, Leiden University)Verified email at gjpvanwesten.nl
