Herman W. T. van Vlijmen - Publications

Affiliations: 
Medicinal Chemistry Leiden University, Leiden, Netherlands 
Area:
Computational Drug Discovery
Website:
https://www.universiteitleiden.nl/en/staffmembers/herman-van-vlijmen

24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Voice AT, Tresadern G, Twidale RM, van Vlijmen H, Mulholland AJ. Mechanism of covalent binding of ibrutinib to Bruton's tyrosine kinase revealed by QM/MM calculations. Chemical Science. 12: 5511-5516. PMID 33995994 DOI: 10.1039/d0sc06122k  0.478
2020 Burggraaff L, van Veen A, Lam CC, Van Vlijmen H, IJzerman AP, van Westen GJP. Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs. Journal of Chemical Information and Modeling. PMID 32931270 DOI: 10.1021/acs.jcim.0c00695  0.518
2020 Goossens K, Wroblowski B, Langini C, van Vlijmen H, Caflisch A, De Winter H. Assessment of the Fragment Docking Program SEED. Journal of Chemical Information and Modeling. PMID 32820916 DOI: 10.1021/Acs.Jcim.0C00556  0.472
2020 Burggraaff L, Lenselink EB, Jespers W, van Engelen J, Bongers BJ, Gorostiola González M, Liu R, Hoos HH, Van Vlijmen H, IJzerman AP, van Westen GJP. Successive Statistical and Structure-Based Modeling to Identify Chemically Novel Kinase Inhibitors. Journal of Chemical Information and Modeling. PMID 32343143 DOI: 10.1021/acs.jcim.9b01204  0.474
2019 Voice A, Tresadern G, Van Vlijmen H, Mulholland AJ. Limitations of ligand-only approaches for predicting the reactivity of covalent inhibitors. Journal of Chemical Information and Modeling. PMID 31498988 DOI: 10.1021/Acs.Jcim.9B00404  0.548
2016 Lenselink EB, Beuming T, van Veen C, Massink A, Sherman W, van Vlijmen HW, IJzerman AP. In search of novel ligands using a structure-based approach: a case study on the adenosine A2A receptor. Journal of Computer-Aided Molecular Design. PMID 27629350 DOI: 10.1007/S10822-016-9963-7  0.548
2016 Lenselink EB, Jespers W, van Vlijmen HW, IJzerman AP, van Westen GJ. Interacting with GPCRs: Using Interaction Fingerprints for Virtual Screening. Journal of Chemical Information and Modeling. 56: 2053-2060. PMID 27626908 DOI: 10.1021/acs.jcim.6b00314  0.736
2014 Lenselink EB, Beuming T, Sherman W, van Vlijmen HW, IJzerman AP. Selecting an optimal number of binding site waters to improve virtual screening enrichments against the adenosine A2A receptor. Journal of Chemical Information and Modeling. 54: 1737-46. PMID 24835542 DOI: 10.1021/Ci5000455  0.45
2013 van Westen GJ, Swier RF, Cortes-Ciriano I, Wegner JK, Overington JP, Ijzerman AP, van Vlijmen HW, Bender A. Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets. Journal of Cheminformatics. 5: 42. PMID 24059743 DOI: 10.1186/1758-2946-5-42  0.741
2013 van Westen GJ, Swier RF, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets. Journal of Cheminformatics. 5: 41. PMID 24059694 DOI: 10.1186/1758-2946-5-41  0.736
2013 van Westen GJ, Hendriks A, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. Plos Computational Biology. 9: e1002899. PMID 23436985 DOI: 10.1371/Journal.Pcbi.1002899  0.742
2012 van Westen GJ, van den Hoven OO, van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, Ijzerman AP, van Vlijmen HW, Bender A. Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data. Journal of Medicinal Chemistry. 55: 7010-20. PMID 22827545 DOI: 10.1021/Jm3003069  0.746
2011 van Westen GJ, Wegner JK, Geluykens P, Kwanten L, Vereycken I, Peeters A, Ijzerman AP, van Vlijmen HW, Bender A. Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development. Plos One. 6: e27518. PMID 22132107 DOI: 10.1371/Journal.Pone.0027518  0.748
2011 van der Horst E, Peironcely JE, van Westen GJ, van den Hoven OO, Galloway WR, Spring DR, Wegner JK, van Vlijmen HW, Ijzerman AP, Overington JP, Bender A. Chemogenomics approaches for receptor deorphanization and extensions of the chemogenomics concept to phenotypic space. Current Topics in Medicinal Chemistry. 11: 1964-77. PMID 21470175 DOI: 10.2174/156802611796391230  0.731
2010 van der Horst E, Peironcely JE, Ijzerman AP, Beukers MW, Lane JR, van Vlijmen HW, Emmerich MT, Okuno Y, Bender A. A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. Bmc Bioinformatics. 11: 316. PMID 20537162 DOI: 10.1186/1471-2105-11-316  0.608
2010 van Westen GJ, Wegner JK, Bender A, Ijzerman AP, van Vlijmen HW. Mining protein dynamics from sets of crystal structures using "consensus structures". Protein Science : a Publication of the Protein Society. 19: 742-52. PMID 20120021 DOI: 10.1002/Pro.350  0.743
2005 van Vlijmen HW, Karplus M. Normal mode calculations of icosahedral viruses with full dihedral flexibility by use of molecular symmetry. Journal of Molecular Biology. 350: 528-42. PMID 15922356 DOI: 10.1016/J.Jmb.2005.03.028  0.345
1998 van Vlijmen HW, Schaefer M, Karplus M. Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure. Proteins. 33: 145-58. PMID 9779784 DOI: 10.1002/(Sici)1097-0134(19981101)33:2<145::Aid-Prot1>3.0.Co;2-I  0.406
1998 van Vlijmen HW, Curry S, Schaefer M, Karplus M. Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH. Journal of Molecular Biology. 275: 295-308. PMID 9466910 DOI: 10.1006/Jmbi.1997.1418  0.351
1997 van Vlijmen HW, Karplus M. PDB-based protein loop prediction: parameters for selection and methods for optimization. Journal of Molecular Biology. 267: 975-1001. PMID 9135125 DOI: 10.1006/Jmbi.1996.0857  0.424
1996 Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins. 23: 318-26. PMID 8710825 DOI: 10.1002/Prot.340230306  0.583
1990 Van Vlijmen HW, Ramé GL, Pettitt BM. A study of model energetics and conformational properties of polynucleotide triplexes. Biopolymers. 30: 517-32. PMID 2265226 DOI: 10.1002/bip.360300505  0.604
1989 van Vlijmen HW, IJzerman AP. Molecular modeling of a putative antagonist binding site on helix III of the beta-adrenoceptor. Journal of Computer-Aided Molecular Design. 3: 165-74. PMID 2570825 DOI: 10.1007/Bf01557726  0.441
1988 IJzerman AP, van Vlijmen HW. A molecular graphics study exploring a putative ligand binding site of the beta-adrenoceptor. Journal of Computer-Aided Molecular Design. 2: 43-53. PMID 2848931 DOI: 10.1007/BF01532052  0.49
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