Albert Jelke Kooistra

Albert Jelke Kooistra

Assistant professor


  1. 3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery

    Kooistra, Albert Jelke, Vass, M., McGuire, R., Leurs, R., de Esch, I. J. P., Vriend, G., Verhoeven, S. & de Graaf, C., 20 Mar 2018, In : ChemMedChem. 13, 6, p. 614-626 13 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  2. 3D-e-Chem-VM: Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine

    McGuire, R., Verhoeven, S., Vass, M., Vriend, G., De Esch, I. J. P., Lusher, S. J., Leurs, R., Ridder, L., Kooistra, Albert Jelke, Ritschel, T. & De Graaf, C., 27 Feb 2017, In : Journal of Chemical Information and Modeling. 57, 2, p. 115-121 7 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  3. Published

    A Structural Framework for GPCR Chemogenomics: What’s In a Residue Number?

    Vass, M., Kooistra, Albert Jelke, Verhoeven, S., Gloriam, David E., de Esch, I. J. P. & de Graaf, C., 1 Jan 2018, Methods in Molecular Biology. Humana Press, p. 73-113 41 p. (Methods in Molecular Biology, Vol. 1705).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  4. A structural chemogenomics analysis of aminergic GPCRs: Lessons for histamine receptor ligand design

    Kooistra, Albert Jelke, Kuhne, S., De Esch, I. J. P., Leurs, R. & De Graaf, C., 1 Sep 2013, In : British Journal of Pharmacology. 170, 1, p. 101-126 26 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  5. Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)

    de Heuvel, E., Singh, A. K., Boronat, P., Kooistra, Albert Jelke, van der Meer, T., Sadek, P., Blaazer, A. R., Shaner, N. C., Bindels, D. S., Caljon, G., Maes, L., Sterk, G. J., Siderius, M., Oberholzer, M., de Esch, I. J. P., Brown, D. G. & Leurs, R., 15 Sep 2019, In : Bioorganic & Medicinal Chemistry. 27, 18, p. 4013-4029 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  6. Published

    Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data

    Vass, M., Podlewska, S., De Esch, I. J. P., Bojarski, A. J., Leurs, R., Kooistra, Albert Jelke & De Graaf, C., 2019, In : Journal of Medicinal Chemistry. 62, 8, p. 3784-3839 56 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  7. Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: Interaction cliffs

    Méndez-Lucio, O., Kooistra, Albert Jelke, Graaf, C. D., Bender, A. & Medina-Franco, J. L., 23 Feb 2015, In : Journal of Chemical Information and Modeling. 55, 2, p. 251-262 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  8. Chemical Diversity in the G Protein-Coupled Receptor Superfamily

    Vass, M., Kooistra, Albert Jelke, Yang, D., Stevens, R. C., Wang, M. W. & de Graaf, C., 1 May 2018, In : Trends in Pharmacological Sciences. 39, 5, p. 494-512 19 p.

    Research output: Contribution to journalReviewResearchpeer-review

  9. Combinatorial consensus scoring for ligand-based virtual fragment screening: A comparative case study for serotonin 5-HT3A, histamine H1, and Histamine H4 receptors

    Schultes, S., Kooistra, Albert Jelke, Vischer, H. F., Nijmeijer, S., Haaksma, E. E. J., Leurs, R., De Esch, I. J. P. & De Graaf, C., 26 May 2015, In : Journal of Chemical Information and Modeling. 55, 5, p. 1030-1034 5 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  10. Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

    AstraZeneca-Sanger Drug Combination DREAM Consortium, A. D. C. D. C., 1 Dec 2019, In : Nature Communications. 10, 1, 17 p., 2674.

    Research output: Contribution to journalJournal articleResearchpeer-review

  11. Covalent Inhibition of the Histamine H3 Receptor

    Wágner, G., Mocking, T. A. M., Kooistra, Albert Jelke, Slynko, I., Ábrányi-Balogh, P., Keserű, G. M., Wijtmans, M., Vischer, H. F., de Esch, I. J. P. & Leurs, R., 11 Dec 2019, In : Molecules (Print Archive Edition). 24, 19 p., 4541.

    Research output: Contribution to journalJournal articleResearchpeer-review

  12. Crystal structure-based virtual screening for fragment-like ligands of the human histamine H 1 receptor

    De Graaf, C., Kooistra, Albert Jelke, Vischer, H. F., Katritch, V., Kuijer, M., Shiroishi, M., Iwata, S., Shimamura, T., Stevens, R. C., De Esch, I. J. P. & Leurs, R., 8 Dec 2011, In : Journal of Medicinal Chemistry. 54, 23, p. 8195-8206 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  13. Development of novel fluorescent histamine H1-receptor antagonists to study ligand-binding kinetics in living cells

    Stoddart, L. A., Vernall, A. J., Bouzo-Lorenzo, M., Bosma, R., Kooistra, Albert Jelke, De Graaf, C., Vischer, H. F., Leurs, R., Briddon, S. J., Kellam, B. & Hill, S. J., 1 Dec 2018, In : Scientific Reports. 8, 1, 1572.

    Research output: Contribution to journalJournal articleResearchpeer-review

  14. Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure

    Jansen, C., Wang, H., Kooistra, Albert Jelke, De Graaf, C., Orrling, K. M., Tenor, H., Seebeck, T., Bailey, D., De Esch, I. J. P., Ke, H. & Leurs, R., 14 Mar 2013, In : Journal of Medicinal Chemistry. 56, 5, p. 2087-2096 10 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  15. Electron density fingerprints (EDprints): Virtual screening using assembled information of electron density

    Kooistra, Albert Jelke, Binsl, T. W., Van Beek, J. H. G. M., De Graaf, C. & Heringa, J., 25 Oct 2010, In : Journal of Chemical Information and Modeling. 50, 10, p. 1772-1780 9 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  16. From heptahelical bundle to hits from the haystack: Structure-based virtual screening for GPCR ligands

    Kooistra, Albert Jelke, Roumen, L., Leurs, R., De Esch, I. J. P. & De Graaf, C., 11 Feb 2013, G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening. p. 279-336 58 p. (Methods in Enzymology, Vol. 522).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  17. From three-dimensional GPCR structure to rational ligand discovery

    Kooistra, Albert Jelke, Leurs, R., De Esch, I. J. P. & Graaf, C. D., 1 Jan 2014, G Protein-Coupled Receptors - Modeling and Simulation. Springer New York LLC, p. 129-157 29 p. (Advances in Experimental Medicine and Biology, Vol. 796).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  18. Function-specific virtual screening for GPCR ligands using a combined scoring method

    Kooistra, Albert Jelke, Vischer, H. F., McNaught-Flores, D., Leurs, R., De Esch, I. J. P. & De Graaf, C., 24 Jun 2016, In : Scientific Reports. 6, 28288.

    Research output: Contribution to journalJournal articleResearchpeer-review

  19. Identification of Ligand Binding Hot Spots of the Histamine H1 Receptor following Structure-Based Fragment Optimization

    Kuhne, S., Kooistra, Albert Jelke, Bosma, R., Bortolato, A., Wijtmans, M., Vischer, H. F., Mason, J. S., De Graaf, C., De Esch, I. J. P. & Leurs, R., 13 Oct 2016, In : Journal of Medicinal Chemistry. 59, 19, p. 9047-9061 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  20. Identification of novel α7 nicotinic receptor ligands by in silico screening against the crystal structure of a chimeric α7 receptor ligand binding domain

    Akdemir, A., Edink, E., Thompson, A. J., Lummis, S. C. R., Kooistra, Albert Jelke, De Graaf, C. & De Esch, I. J. P., 1 Oct 2012, In : Bioorganic and Medicinal Chemistry. 20, 19, p. 5992-6002 11 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  21. KLIFS: A structural kinase-ligand interaction database

    Kooistra, Albert Jelke, Kanev, G. K., Van Linden, O. P. J., Leurs, R., De Esch, I. J. P. & De Graaf, C., 1 Jan 2016, In : Nucleic Acids Research. 44, D1, p. D365-D371

    Research output: Contribution to journalJournal articleResearchpeer-review

  22. KLIFS: A knowledge-based structural database to navigate kinase-ligand interaction space

    Van Linden, O. P. J., Kooistra, Albert Jelke, Leurs, R., De Esch, I. J. P. & De Graaf, C., 23 Jan 2014, In : Journal of Medicinal Chemistry. 57, 2, p. 249-277 29 p.

    Research output: Contribution to journalReviewResearchpeer-review

  23. Kinase-Centric Computational Drug Development

    Kooistra, Albert Jelke & Volkamer, A., 1 Jan 2017, Annual Reports in Medicinal Chemistry. Academic Press, p. 263-299 37 p. (Annual Reports in Medicinal Chemistry, Vol. 50).

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  24. Mapping histamine H4 receptor-ligand binding modes

    Schultes, S., Nijmeijer, S., Engelhardt, H., Kooistra, Albert Jelke, Vischer, H. F., De Esch, I. J. P., Haaksma, E. E. J., Leurs, R. & De Graaf, C., 1 Jan 2013, In : MedChemComm. 4, 1, p. 193-204 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  25. Molecular determinants of ligand binding modes in the histamine H 4 receptor: Linking ligand-based three-dimensional quantitative structure-activity relationship (3D-QSAR) models to in silico guided receptor mutagenesis studies

    Istyastono, E. P., Nijmeijer, S., Lim, H. D., Van De Stolpe, A., Roumen, L., Kooistra, Albert Jelke, Vischer, H. F., De Esch, I. J. P., Leurs, R. & De Graaf, C., 8 Dec 2011, In : Journal of Medicinal Chemistry. 54, 23, p. 8136-8147 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  26. Molecular interaction fingerprint approaches for GPCR drug discovery

    Vass, M., Kooistra, Albert Jelke, Ritschel, T., Leurs, R., de Esch, I. J. & de Graaf, C., 1 Oct 2016, In : Current Opinion in Pharmacology. 30, p. 59-68 10 p.

    Research output: Contribution to journalReviewResearchpeer-review

  27. PDEStrIAn: A Phosphodiesterase Structure and Ligand Interaction Annotated Database As a Tool for Structure-Based Drug Design

    Jansen, C., Kooistra, Albert Jelke, Kanev, G. K., Leurs, R., De Esch, I. J. P. & De Graaf, C., 11 Aug 2016, In : Journal of Medicinal Chemistry. 59, 15, p. 7029-7065 37 p.

    Research output: Contribution to journalReviewResearchpeer-review

  28. Route to Prolonged Residence Time at the Histamine H1 Receptor: Growing from Desloratadine to Rupatadine

    Bosma, R., Wang, Z., Kooistra, Albert Jelke, Bushby, N., Kuhne, S., van den Bor, J., Waring, M. J., de Graaf, C., de Esch, I. J., Vischer, H. F., Sheppard, R. J., Wijtmans, M. & Leurs, R., 25 Jul 2019, In : Journal of Medicinal Chemistry. 62, 14, p. 6630-6644 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  29. Small and colorful stones make beautiful mosaics: Fragment-based chemogenomics

    De Graaf, C., Vischer, H. F., De Kloe, G. E., Kooistra, Albert Jelke, Nijmeijer, S., Kuijer, M., Verheij, M. H. P., England, P. J., Van Muijlwijk-Koezen, J. E., Leurs, R. & De Esch, I. J. P., 1 Apr 2013, In : Drug Discovery Today. 18, 7-8, p. 323-330 8 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  30. Structural Chemogenomics Databases to Navigate Protein-Ligand Interaction Space

    Kanev, G. K., Kooistra, Albert Jelke, de Esch, I. J. P. & de Graaf, C., 3 Jun 2017, The Future of Drug Discovery. Elsevier Science Inc., Vol. 1-8. p. 444-471 28 p.

    Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

  31. Structural insights into serotonin receptor ligands polypharmacology

    Podlewska, S., Kafel, R., Lacivita, E., Satała, G., Kooistra, Albert Jelke, Vass, M., de Graaf, C., Leopoldo, M., Bojarski, A. J. & Mordalski, Stefan Mateusz, 10 May 2018, In : European Journal of Medicinal Chemistry. 151, p. 797-814 18 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  32. Structure-based prediction of g-protein-coupled receptor ligand function: A β-adrenoceptor case study

    Kooistra, Albert Jelke, Leurs, R., De Esch, I. J. P. & De Graaf, C., 26 May 2015, In : Journal of Chemical Information and Modeling. 55, 5, p. 1045-1061 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  33. Structure-based virtual screening for fragment-like ligands of the G protein-coupled histamine H4 receptor

    Istyastono, E. P., Istyastono, E. P., Kooistra, Albert Jelke, Vischer, H. F., Kuijer, M., Roumen, L., Nijmeijer, S., Smits, R. A., De Esch, I. J. P., Leurs, R. & De Graaf, C., 1 Jun 2015, In : MedChemComm. 6, 6, p. 1003-1017 15 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  34. Synthesis and Characterization of a Bidirectional Photoswitchable Antagonist Toolbox for Real-Time GPCR Photopharmacology

    Hauwert, N. J., Mocking, T. A. M., Da Costa Pereira, D., Kooistra, Albert Jelke, Wijnen, L. M., Vreeker, G. C. M., Verweij, E. W. E., De Boer, A. H., Smit, M. J., De Graaf, C., Vischer, H. F., De Esch, I. J. P., Wijtmans, M. & Leurs, R., 28 Mar 2018, In : Journal of the American Chemical Society. 140, 12, p. 4232-4243 12 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

  35. The Landscape of Atypical and Eukaryotic Protein Kinases

    Kanev, G. K., de Graaf, C., de Esch, I. J. P., Leurs, R., Würdinger, T., Westerman, B. A. & Kooistra, Albert Jelke, Nov 2019, In : Trends in Pharmacological Sciences. 40, 11, p. 818-832 15 p.

    Research output: Contribution to journalReviewResearchpeer-review

  36. The Receptor Concept in 3D: From Hypothesis and Metaphor to GPCR–Ligand Structures

    Kooistra, Albert Jelke, de Graaf, C. & Timmerman, H., 1 Jan 2014, In : Neurochemical Research. 39, 10, p. 1850-1861 12 p.

    Research output: Contribution to journalReviewResearchpeer-review

  37. The viral G protein-coupled receptor ORF74 hijacks β-arrestins for endocytic trafficking in response to human chemokines

    De Munnik, S. M., Kooistra, Albert Jelke, Van Offenbeek, J., Nijmeijer, S., De Graaf, C., Smit, M. J., Leurs, R. & Vischer, H. F., 20 Apr 2015, In : PLOS ONE. 10, 4, e0124486.

    Research output: Contribution to journalJournal articleResearchpeer-review

  38. E-pub ahead of print

    Utilizing drug-target-event relationships to unveil safety patterns in pharmacovigilance

    Hauser, Alexander Sebastian, Kooistra, Albert Jelke, Sverrisdóttir, Eva & Sessa, Maurizio, 8 Jun 2020, In : Expert Opinion on Drug Safety.

    Research output: Contribution to journalJournal articleResearchpeer-review

  39. Virtual fragment screening: Discovery of histamine H3 receptor ligands using ligand-based and protein-based molecular fingerprints

    Sirci, F., Istyastono, E. P., Istyastono, E. P., Vischer, H. F., Kooistra, Albert Jelke, Nijmeijer, S., Kuijer, M., Wijtmans, M., Mannhold, R., Leurs, R., De Esch, I. J. P. & De Graaf, C., 21 Dec 2012, In : Journal of Chemical Information and Modeling. 52, 12, p. 3308-3324 17 p.

    Research output: Contribution to journalJournal articleResearchpeer-review

ID: 196033213