Albert Jelke Kooistra

Albert Jelke Kooistra

Assistant professor

Member of:


    1. 3D-e-Chem : Structural Cheminformatics Workflows for Computer-Aided Drug Discovery. / Kooistra, Albert J.; Vass, Márton; McGuire, Ross; Leurs, Rob; de Esch, Iwan J.P.; Vriend, Gert; Verhoeven, Stefan; de Graaf, Chris.

      In: ChemMedChem, Vol. 13, No. 6, 20.03.2018, p. 614-626.

      Research output: Contribution to journalJournal articleResearchpeer-review

    2. 3D-e-Chem-VM : Structural Cheminformatics Research Infrastructure in a Freely Available Virtual Machine. / McGuire, Ross; Verhoeven, Stefan; Vass, Márton; Vriend, Gerrit; De Esch, Iwan J.P.; Lusher, Scott J.; Leurs, Rob; Ridder, Lars; Kooistra, Albert J.; Ritschel, Tina; De Graaf, Chris.

      In: Journal of Chemical Information and Modeling, Vol. 57, No. 2, 27.02.2017, p. 115-121.

      Research output: Contribution to journalJournal articleResearchpeer-review

    3. Published

      A Structural Framework for GPCR Chemogenomics : What’s In a Residue Number? / Vass, Márton; Kooistra, Albert J.; Verhoeven, Stefan; Gloriam, David; de Esch, Iwan J.P.; de Graaf, Chris.

      Methods in Molecular Biology. Humana Press, 2018. p. 73-113 (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, A. J.; Kuhne, S.; De Esch, I. J.P.; Leurs, R.; De Graaf, C.

      In: British Journal of Pharmacology, Vol. 170, No. 1, 01.09.2013, p. 101-126.

      Research output: Contribution to journalJournal articleResearchpeer-review

    5. 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, A.J.; De Graaf, C.

      In: Journal of Medicinal Chemistry, Vol. 62, No. 8, 2019, p. 3784-3839.

      Research output: Contribution to journalJournal articleResearchpeer-review

    6. Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints : Interaction cliffs. / Méndez-Lucio, Oscar; Kooistra, Albert J.; Graaf, Chris De; Bender, Andreas; Medina-Franco, José L.

      In: Journal of Chemical Information and Modeling, Vol. 55, No. 2, 23.02.2015, p. 251-262.

      Research output: Contribution to journalJournal articleResearchpeer-review

    7. Chemical Diversity in the G Protein-Coupled Receptor Superfamily. / Vass, Márton; Kooistra, Albert J.; Yang, Dehua; Stevens, Raymond C.; Wang, Ming Wei; de Graaf, Chris.

      In: Trends in Pharmacological Sciences, Vol. 39, No. 5, 01.05.2018, p. 494-512.

      Research output: Contribution to journalReviewResearchpeer-review

    8. Combinatorial consensus scoring for ligand-based virtual fragment screening : A comparative case study for serotonin 5-HT3A, histamine H1, and Histamine H4 receptors. / Schultes, Sabine; Kooistra, Albert J.; Vischer, Henry F.; Nijmeijer, Saskia; Haaksma, Eric E.J.; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

      In: Journal of Chemical Information and Modeling, Vol. 55, No. 5, 26.05.2015, p. 1030-1034.

      Research output: Contribution to journalJournal articleResearchpeer-review

    9. Crystal structure-based virtual screening for fragment-like ligands of the human histamine H 1 receptor. / De Graaf, Chris; Kooistra, Albert J.; Vischer, Henry F.; Katritch, Vsevolod; Kuijer, Martien; Shiroishi, Mitsunori; Iwata, So; Shimamura, Tatsuro; Stevens, Raymond C.; De Esch, Iwan J P; Leurs, Rob.

      In: Journal of Medicinal Chemistry, Vol. 54, No. 23, 08.12.2011, p. 8195-8206.

      Research output: Contribution to journalJournal articleResearchpeer-review

    10. Development of novel fluorescent histamine H1-receptor antagonists to study ligand-binding kinetics in living cells. / Stoddart, Leigh A.; Vernall, Andrea J.; Bouzo-Lorenzo, Monica; Bosma, Reggie; Kooistra, Albert J.; De Graaf, Chris; Vischer, Henry F.; Leurs, Rob; Briddon, Stephen J.; Kellam, Barrie; Hill, Stephen J.

      In: Scientific Reports, Vol. 8, No. 1, 1572, 01.12.2018.

      Research output: Contribution to journalJournal articleResearchpeer-review

    11. Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure. / Jansen, Chimed; Wang, Huanchen; Kooistra, Albert J.; De Graaf, Chris; Orrling, Kristina M.; Tenor, Hermann; Seebeck, Thomas; Bailey, David; De Esch, Iwan J.P.; Ke, Hengming; Leurs, Rob.

      In: Journal of Medicinal Chemistry, Vol. 56, No. 5, 14.03.2013, p. 2087-2096.

      Research output: Contribution to journalJournal articleResearchpeer-review

    12. Electron density fingerprints (EDprints) : Virtual screening using assembled information of electron density. / Kooistra, Albert J.; Binsl, Thomas W.; Van Beek, Johannes H.G.M.; De Graaf, Chris; Heringa, Jaap.

      In: Journal of Chemical Information and Modeling, Vol. 50, No. 10, 25.10.2010, p. 1772-1780.

      Research output: Contribution to journalJournal articleResearchpeer-review

    13. From heptahelical bundle to hits from the haystack : Structure-based virtual screening for GPCR ligands. / Kooistra, Albert J.; Roumen, Luc; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

      G Protein Coupled ReceptorsModeling, Activation, Interactions and Virtual Screening. 2013. p. 279-336 (Methods in Enzymology, Vol. 522).

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

    14. From three-dimensional GPCR structure to rational ligand discovery. / Kooistra, Albert J.; Leurs, Rob; De Esch, Iwan J.P.; Graaf, Chris De.

      G Protein-Coupled Receptors - Modeling and Simulation. Springer New York LLC, 2014. p. 129-157 (Advances in Experimental Medicine and Biology, Vol. 796).

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

    15. Function-specific virtual screening for GPCR ligands using a combined scoring method. / Kooistra, Albert J.; Vischer, Henry F.; McNaught-Flores, Daniel; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

      In: Scientific Reports, Vol. 6, 28288, 24.06.2016.

      Research output: Contribution to journalJournal articleResearchpeer-review

    16. Identification of Ligand Binding Hot Spots of the Histamine H1 Receptor following Structure-Based Fragment Optimization. / Kuhne, Sebastiaan; Kooistra, Albert J.; Bosma, Reggie; Bortolato, Andrea; Wijtmans, Maikel; Vischer, Henry F.; Mason, Jonathan S.; De Graaf, Chris; De Esch, Iwan J.P.; Leurs, Rob.

      In: Journal of Medicinal Chemistry, Vol. 59, No. 19, 13.10.2016, p. 9047-9061.

      Research output: Contribution to journalJournal articleResearchpeer-review

    17. Identification of novel α7 nicotinic receptor ligands by in silico screening against the crystal structure of a chimeric α7 receptor ligand binding domain. / Akdemir, Atilla; Edink, Ewald; Thompson, Andrew J.; Lummis, Sarah C.R.; Kooistra, Albert J.; De Graaf, Chris; De Esch, Iwan J.P.

      In: Bioorganic and Medicinal Chemistry, Vol. 20, No. 19, 01.10.2012, p. 5992-6002.

      Research output: Contribution to journalJournal articleResearchpeer-review

    18. KLIFS : A structural kinase-ligand interaction database. / Kooistra, Albert J.; Kanev, Georgi K.; Van Linden, Oscar P.J.; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

      In: Nucleic Acids Research, Vol. 44, No. D1, 01.01.2016, p. D365-D371.

      Research output: Contribution to journalJournal articleResearchpeer-review

    19. KLIFS : A knowledge-based structural database to navigate kinase-ligand interaction space. / Van Linden, Oscar P.J.; Kooistra, Albert J.; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

      In: Journal of Medicinal Chemistry, Vol. 57, No. 2, 23.01.2014, p. 249-277.

      Research output: Contribution to journalReviewResearchpeer-review

    20. Kinase-Centric Computational Drug Development. / Kooistra, Albert J.; Volkamer, Andrea.

      Annual Reports in Medicinal Chemistry. Academic Press, 2017. p. 263-299 (Annual Reports in Medicinal Chemistry, Vol. 50).

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

    21. Mapping histamine H4 receptor-ligand binding modes. / Schultes, Sabine; Nijmeijer, Saskia; Engelhardt, Harald; Kooistra, Albert J.; Vischer, Henry F.; De Esch, Iwan J P; Haaksma, Eric E J; Leurs, Rob; De Graaf, Chris.

      In: MedChemComm, Vol. 4, No. 1, 01.01.2013, p. 193-204.

      Research output: Contribution to journalJournal articleResearchpeer-review

    22. 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, Enade P.; Nijmeijer, Saskia; Lim, Herman D.; Van De Stolpe, Andrea; Roumen, Luc; Kooistra, Albert J.; Vischer, Henry F.; De Esch, Iwan J.P.; Leurs, Rob; De Graaf, Chris.

      In: Journal of Medicinal Chemistry, Vol. 54, No. 23, 08.12.2011, p. 8136-8147.

      Research output: Contribution to journalJournal articleResearchpeer-review

    23. Molecular interaction fingerprint approaches for GPCR drug discovery. / Vass, Márton; Kooistra, Albert J.; Ritschel, Tina; Leurs, Rob; de Esch, Iwan JP; de Graaf, Chris.

      In: Current Opinion in Pharmacology, Vol. 30, 01.10.2016, p. 59-68.

      Research output: Contribution to journalReviewResearchpeer-review

    24. PDEStrIAn : A Phosphodiesterase Structure and Ligand Interaction Annotated Database As a Tool for Structure-Based Drug Design. / Jansen, Chimed; Kooistra, Albert J.; Kanev, Georgi K.; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

      In: Journal of Medicinal Chemistry, Vol. 59, No. 15, 11.08.2016, p. 7029-7065.

      Research output: Contribution to journalReviewResearchpeer-review

    25. Small and colorful stones make beautiful mosaics : Fragment-based chemogenomics. / De Graaf, Chris; Vischer, Henry F.; De Kloe, Gerdien E.; Kooistra, Albert J.; Nijmeijer, Saskia; Kuijer, Martien; Verheij, Mark H.P.; England, Paul J.; Van Muijlwijk-Koezen, Jacqueline E.; Leurs, Rob; De Esch, Iwan J.P.

      In: Drug Discovery Today, Vol. 18, No. 7-8, 01.04.2013, p. 323-330.

      Research output: Contribution to journalJournal articleResearchpeer-review

    26. Structural Chemogenomics Databases to Navigate Protein-Ligand Interaction Space. / Kanev, G. K.; Kooistra, A. J.; de Esch, I. J.P.; de Graaf, C.

      The Future of Drug Discovery. Vol. 1-8 Elsevier Science Inc., 2017. p. 444-471.

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

    27. Structural insights into serotonin receptor ligands polypharmacology. / Podlewska, Sabina; Kafel, Rafał; Lacivita, Enza; Satała, Grzegorz; Kooistra, Albert J.; Vass, Márton; de Graaf, Chris; Leopoldo, Marcello; Bojarski, Andrzej J.; Mordalski, Stefan.

      In: European Journal of Medicinal Chemistry, Vol. 151, 10.05.2018, p. 797-814.

      Research output: Contribution to journalJournal articleResearchpeer-review

    28. Structure-based prediction of g-protein-coupled receptor ligand function : A β-adrenoceptor case study. / Kooistra, Albert J.; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

      In: Journal of Chemical Information and Modeling, Vol. 55, No. 5, 26.05.2015, p. 1045-1061.

      Research output: Contribution to journalJournal articleResearchpeer-review

    29. Structure-based virtual screening for fragment-like ligands of the G protein-coupled histamine H4 receptor. / Istyastono, Enade P.; Istyastono, Enade P.; Kooistra, Albert J.; Vischer, Henry F.; Kuijer, Martien; Roumen, Luc; Nijmeijer, Saskia; Smits, Rogier A.; De Esch, Iwan J.P.; Leurs, Rob; De Graaf, Chris.

      In: MedChemComm, Vol. 6, No. 6, 01.06.2015, p. 1003-1017.

      Research output: Contribution to journalJournal articleResearchpeer-review

    30. Synthesis and Characterization of a Bidirectional Photoswitchable Antagonist Toolbox for Real-Time GPCR Photopharmacology. / Hauwert, Niels J.; Mocking, Tamara A.M.; Da Costa Pereira, Daniel; Kooistra, Albert J.; Wijnen, Lisa M.; Vreeker, Gerda C.M.; Verweij, Eléonore W.E.; De Boer, Albertus H.; Smit, Martine J.; De Graaf, Chris; Vischer, Henry F.; De Esch, Iwan J.P.; Wijtmans, Maikel; Leurs, Rob.

      In: Journal of the American Chemical Society, Vol. 140, No. 12, 28.03.2018, p. 4232-4243.

      Research output: Contribution to journalJournal articleResearchpeer-review

    31. The Receptor Concept in 3D : From Hypothesis and Metaphor to GPCR–Ligand Structures. / Kooistra, Albert J.; de Graaf, Chris; Timmerman, Henk.

      In: Neurochemical Research, Vol. 39, No. 10, 01.01.2014, p. 1850-1861.

      Research output: Contribution to journalReviewResearchpeer-review

    32. The viral G protein-coupled receptor ORF74 hijacks β-arrestins for endocytic trafficking in response to human chemokines. / De Munnik, Sabrina M.; Kooistra, Albert J.; Van Offenbeek, Jody; Nijmeijer, Saskia; De Graaf, Chris; Smit, Martine J.; Leurs, Rob; Vischer, Henry F.

      In: PLOS ONE, Vol. 10, No. 4, e0124486, 20.04.2015.

      Research output: Contribution to journalJournal articleResearchpeer-review

    33. Virtual fragment screening : Discovery of histamine H3 receptor ligands using ligand-based and protein-based molecular fingerprints. / Sirci, Francesco; Istyastono, Enade P.; Istyastono, Enade P.; Vischer, Henry F.; Kooistra, Albert J.; Nijmeijer, Saskia; Kuijer, Martien; Wijtmans, Maikel; Mannhold, Raimund; Leurs, Rob; De Esch, Iwan J.P.; De Graaf, Chris.

      In: Journal of Chemical Information and Modeling, Vol. 52, No. 12, 21.12.2012, p. 3308-3324.

      Research output: Contribution to journalJournal articleResearchpeer-review

    ID: 196033213