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

41 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
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  0.96
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  0.36
2020 Deflorian F, Perez-Benito L, Lenselink EB, Congreve M, van Vlijmen HWT, Mason JS, Graaf C, Tresadern G. Accurate Prediction of GPCR Ligand Binding Affinity with Free Energy Perturbation. Journal of Chemical Information and Modeling. PMID 32539374 DOI: 10.1021/acs.jcim.0c00449  0.72
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  0.96
2019 Liu X, Ye K, van Vlijmen HWT, IJzerman AP, van Westen GJP. An exploration strategy improves the diversity of de novo ligands using deep reinforcement learning: a case for the adenosine A receptor. Journal of Cheminformatics. 11: 35. PMID 31127405 DOI: 10.1186/s13321-019-0355-6  0.96
2019 Sydow D, Burggraaff L, Szengel A, van Vlijmen HWT, IJzerman AP, van Westen GJP, Volkamer A. Advances and Challenges in Computational Target Prediction. Journal of Chemical Information and Modeling. PMID 30817146 DOI: 10.1021/acs.jcim.8b00832  0.96
2018 Ghanakota P, Van Vlijmen HWT, Sherman W, Beuming T. Large Scale Validation of Mixed-Solvent Simulations to Assess Hotspots at PPI Interfaces. Journal of Chemical Information and Modeling. PMID 29617116 DOI: 10.1021/Acs.Jcim.7B00487  0.52
2017 Tresadern G, Trabanco AA, Pérez-Benito L, Overington JP, van Vlijmen HWT, van Westen GJP. Identification of Allosteric Modulators of Metabotropic Glutamate 7 Receptor Using Proteochemometric Modeling. Journal of Chemical Information and Modeling. PMID 29172488 DOI: 10.1021/acs.jcim.7b00338  0.8
2017 Lenselink EB, Ten Dijke N, Bongers B, Papadatos G, van Vlijmen HWT, Kowalczyk W, IJzerman AP, van Westen GJP. Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set. Journal of Cheminformatics. 9: 45. PMID 29086168 DOI: 10.1186/s13321-017-0232-0  0.96
2016 Lenselink EB, Louvel J, Forti AF, van Veldhoven JPD, de Vries H, Mulder-Krieger T, McRobb FM, Negri A, Goose J, Abel R, van Vlijmen HWT, Wang L, Harder E, Sherman W, IJzerman AP, et al. Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation. Acs Omega. 1: 293-304. PMID 30023478 DOI: 10.1021/acsomega.6b00086  0.96
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  0.96
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  0.96
2015 Jacoby E, Tresadern G, Bembenek S, Wroblowski B, Buyck C, Neefs JM, Rassokhin D, Poncelet A, Hunt J, van Vlijmen H. Extending kinome coverage by analysis of kinase inhibitor broad profiling data. Drug Discovery Today. 20: 652-8. PMID 25596550 DOI: 10.1016/j.drudis.2015.01.002  0.84
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  0.84
2014 Clark LA, Demarest SJ, Eldredge J, Jarpe MB, Li Y, Simon K, van Vlijmen HW. Influence of canonical structure determining residues on antibody affinity and stability. Journal of Structural Biology. 185: 223-7. PMID 23994046 DOI: 10.1016/J.Jsb.2013.08.009  0.84
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  0.84
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  0.96
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
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  0.84
2010 Roymans D, De Bondt HL, Arnoult E, Geluykens P, Gevers T, Van Ginderen M, Verheyen N, Kim H, Willebrords R, Bonfanti JF, Bruinzeel W, Cummings MD, van Vlijmen H, Andries K. Binding of a potent small-molecule inhibitor of six-helix bundle formation requires interactions with both heptad-repeats of the RSV fusion protein. Proceedings of the National Academy of Sciences of the United States of America. 107: 308-13. PMID 19966279 DOI: 10.1073/pnas.0910108106  0.84
2009 Clark LA, Boriack-Sjodin PA, Day E, Eldredge J, Fitch C, Jarpe M, Miller S, Li Y, Simon K, van Vlijmen HW. An antibody loop replacement design feasibility study and a loop-swapped dimer structure. Protein Engineering, Design & Selection : Peds. 22: 93-101. PMID 19074157 DOI: 10.1093/Protein/Gzn072  0.84
2008 Lin EY, Guckian KM, Silvian L, Chin D, Boriack-Sjodin PA, van Vlijmen H, Friedman JE, Scott DM. Structure-activity relationship of ortho- and meta-phenol based LFA-1 ICAM inhibitors. Bioorganic & Medicinal Chemistry Letters. 18: 5245-8. PMID 18783948 DOI: 10.1016/j.bmcl.2008.08.062  0.84
2008 Clark LA, van Vlijmen HW. A knowledge-based forcefield for protein-protein interface design. Proteins. 70: 1540-50. PMID 17910054 DOI: 10.1002/Prot.21694  0.84
2006 Clark LA, Ganesan S, Papp S, van Vlijmen HW. Trends in antibody sequence changes during the somatic hypermutation process. Journal of Immunology (Baltimore, Md. : 1950). 177: 333-40. PMID 16785529 DOI: 10.4049/Jimmunol.177.1.333  0.84
2006 Reid C, Rushe M, Jarpe M, van Vlijmen H, Dolinski B, Qian F, Cachero TG, Cuervo H, Yanachkova M, Nwankwo C, Wang X, Etienne N, Garber E, Bailly V, de Fougerolles A, et al. Structure activity relationships of monocyte chemoattractant proteins in complex with a blocking antibody. Protein Engineering, Design & Selection : Peds. 19: 317-24. PMID 16682434 DOI: 10.1093/protein/gzl015  0.84
2006 Clark LA, Boriack-Sjodin PA, Eldredge J, Fitch C, Friedman B, Hanf KJ, Jarpe M, Liparoto SF, Li Y, Lugovskoy A, Miller S, Rushe M, Sherman W, Simon K, Van Vlijmen H. Affinity enhancement of an in vivo matured therapeutic antibody using structure-based computational design. Protein Science : a Publication of the Protein Society. 15: 949-60. PMID 16597831 DOI: 10.1110/Ps.052030506  0.84
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  0.84
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  1
1998 Schaefer M, van Vlijmen HW, Karplus M. Electrostatic contributions to molecular free energies in solution. Advances in Protein Chemistry. 51: 1-57. PMID 9615168 DOI: 10.1016/S0065-3233(08)60650-6  1
1998 Singh J, Garber E, Van Vlijmen H, Karpusas M, Hsu YM, Zheng Z, Naismith JH, Thomas D. The role of polar interactions in the molecular recognition of CD40L with its receptor CD40 Protein Science. 7: 1124-1135. PMID 9605317  0.84
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  1
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  1
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  0.36
1990 Van Galen PJM, Van Vlijmen HWT, IJzerman AP, Soudijn W. A model for the antagonist binding site on the adenosine A1 receptor, based on steric, electrostatic, and hydrophobic properties Journal of Medicinal Chemistry. 33: 1708-1713. PMID 2342066 DOI: 10.1021/jm00168a027  0.84
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  0.96
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  0.96
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  0.96
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