Albert J. Kooistra
Associate Professor
Pharmaceutical Informatics
Universitetsparken 2
2100 København Ø
3D-e-Chem: Structural Cheminformatics Workflows for Computer-Aided Drug Discovery
Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
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 J., 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 journal › Journal article › Research › peer-review
- Published
A Structural Framework for GPCR Chemogenomics: What’s In a Residue Number?
Vass, M., Kooistra, Albert J., 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 proceeding › Book chapter › Research › peer-review
- Published
A community Biased Signaling Atlas
Caroli, J., Mamyrbekov, A., Harpsøe, Kasper, Gardizi, S., Dörries, L., Ghosh, E., Hauser, Alexander Sebastian, Kooistra, Albert J. & Gloriam, David E., 2023, In: Nature Chemical Biology. 19, p. 531–535Research output: Contribution to journal › Comment/debate › Research › peer-review
A structural chemogenomics analysis of aminergic GPCRs: Lessons for histamine receptor ligand design
Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2)
de Heuvel, E., Singh, A. K., Boronat, P., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
- 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 J. & De Graaf, C., 2019, In: Journal of Medicinal Chemistry. 62, 8, p. 3784-3839 56 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
An online GPCR structure analysis platform
Kooistra, Albert J., Munk, C., Hauser, Alexander Sebastian & Gloriam, David E., 2021, In: Nature Structural and Molecular Biology. 28, 11, p. 875-878Research output: Contribution to journal › Journal article › Research › peer-review
Analyzing multitarget activity landscapes using protein-ligand interaction fingerprints: Interaction cliffs
Méndez-Lucio, O., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
Chemical Diversity in the G Protein-Coupled Receptor Superfamily
Vass, M., Kooistra, Albert J., 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 journal › Review › Research › peer-review
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 J., 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 journal › Journal article › Research › peer-review
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 journal › Journal article › Research › peer-review
Covalent Inhibition of the Histamine H3 Receptor
Wágner, G., Mocking, T. A. M., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
Crystal structure-based virtual screening for fragment-like ligands of the human histamine H 1 receptor
De Graaf, C., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
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 J., 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 journal › Journal article › Research › peer-review
- Published
Differential GLP-1R Binding and Activation by Peptide and Non-peptide Agonists
Zhang, X., Belousoff, M. J., Zhao, P., Kooistra, A. J., Truong, T. T., Ang, S. Y., Underwood, C. R., Egebjerg, T., Šenel, P., Stewart, G. D., Liang, Y-L., Glukhova, A., Venugopal, H., Christopoulos, A., Furness, S. G. B., Miller, L. J., Reedtz-Runge, S., Langmead, C. J., Gloriam, D. E., Danev, R. & 2 others, , 2020, In: Molecular Cell. 80, 3, p. 485-500Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discovery of Diaryl Ether Substituted Tetrahydrophthalazinones as TbrPDEB1 Inhibitors Following Structure-Based Virtual Screening
de Heuvel, E., Kooistra, Albert J., Edink, E., van Klaveren, S., Stuijt, J., van der Meer, T., Sadek, P., Mabille, D., Caljon, G., Maes, L., Siderius, M., de Esch, I. J. P., Sterk, G. J. & Leurs, R., 21 Jan 2021, In: Frontiers in Chemistry. 8, 10 p., 608030.Research output: Contribution to journal › Journal article › Research › peer-review
Discovery of novel Trypanosoma brucei phosphodiesterase B1 inhibitors by virtual screening against the unliganded TbrPDEB1 crystal structure
Jansen, C., Wang, H., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
Electron density fingerprints (EDprints): Virtual screening using assembled information of electron density
Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
From heptahelical bundle to hits from the haystack: Structure-based virtual screening for GPCR ligands
Kooistra, Albert J., 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 proceeding › Book chapter › Research › peer-review
From three-dimensional GPCR structure to rational ligand discovery
Kooistra, Albert J., 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 proceeding › Book chapter › Research › peer-review
Function-specific virtual screening for GPCR ligands using a combined scoring method
Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
- Published
GPCR activation mechanisms across classes and macro/microscales
Hauser, Alexander Sebastian, Kooistra, Albert J., Munk, C., Heydenreich, F. M., Veprintsev, D. B., Bouvier, M., Babu, M. M. & Gloriam, David E., 2021, In: Nature Structural and Molecular Biology. 28, 11, p. 879-888Research output: Contribution to journal › Journal article › Research › peer-review
- Published
GPCRdb in 2021: integrating GPCR sequence, structure and function
Kooistra, Albert J., Mordalski, S., Pándy-Szekeres, Gáspár, Esguerra, M., Mamyrbekov, A., Munk, C., Keserű, G. M. & Gloriam, David E., 2021, In: Nucleic Acids Research. 49, D1, p. D335-D343Research output: Contribution to journal › Journal article › Research › peer-review
- Published
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources
Pándy-Szekeres, Gáspár, Caroli, J., Mamyrbekov, A., Kermani, A. A., Keserű, G. M., Kooistra, Albert J. & Gloriam, David E., 2023, In: Nucleic Acids Research. 51, D1, p. D395–D402Research output: Contribution to journal › Journal article › Research › peer-review
Identification of Ligand Binding Hot Spots of the Histamine H1 Receptor following Structure-Based Fragment Optimization
Kuhne, S., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
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 J., 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 journal › Journal article › Research › peer-review
- Published
KLIFS: an overhaul after the first 5 years of supporting kinase research
Kanev, G. K., de Graaf, C., Westerman, B. A., de Esch, I. J. P. & Kooistra, Albert J., 2021, In: Nucleic Acids Research. 49, D1, p. D562-D569Research output: Contribution to journal › Journal article › Research › peer-review
KLIFS: A knowledge-based structural database to navigate kinase-ligand interaction space
Van Linden, O. P. J., Kooistra, Albert J., 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 journal › Review › Research › peer-review
KLIFS: A structural kinase-ligand interaction database
Kooistra, Albert J., 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-D371Research output: Contribution to journal › Journal article › Research › peer-review
- Published
KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome
Sydow, D., Aßmann, E., Kooistra, Albert J., Rippmann, F. & Volkamer, A., 2022, In: Journal of Chemical Information and Modeling. 62, 10, p. 2600–2616Research output: Contribution to journal › Journal article › Research › peer-review
Kinase-Centric Computational Drug Development
Kooistra, Albert J. & 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 proceeding › Book chapter › Research › peer-review
Mapping histamine H4 receptor-ligand binding modes
Schultes, S., Nijmeijer, S., Engelhardt, H., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
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 J., 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 journal › Journal article › Research › peer-review
Molecular interaction fingerprint approaches for GPCR drug discovery
Vass, M., Kooistra, Albert J., 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 journal › Review › Research › peer-review
PDEStrIAn: A Phosphodiesterase Structure and Ligand Interaction Annotated Database As a Tool for Structure-Based Drug Design
Jansen, C., Kooistra, Albert J., 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 journal › Review › Research › peer-review
- Published
Pharmacological Characterization of the Zebrafish (Danio Rerio) Histamine H1 Receptor Reveals the Involvement of the Second Extracellular Loop in the Binding of Histamine
McNaught-Flores, D. A., Kooistra, Albert J., Chen, Y. C., Arias-Montano, J. A., Panula, P. & Leurs, R., 2024, In: Molecular Pharmacology. 105, 2, p. 84-96Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Predicting the target landscape of kinase inhibitors using 3D convolutional neural networks
Kanev, G. K., Zhang, Y., Kooistra, Albert J., Bender, A., Leurs, R., Bailey, D., Würdinger, T., Graaf, C. D., de Esch, I. J. P. & Westerman, B. A., 2023, In: PLOS Computational Biology. 19, 9, 19 p., e1011301.Research output: Contribution to journal › Journal article › Research › peer-review
Route to Prolonged Residence Time at the Histamine H1 Receptor: Growing from Desloratadine to Rupatadine
Bosma, R., Wang, Z., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
Small and colorful stones make beautiful mosaics: Fragment-based chemogenomics
De Graaf, C., Vischer, H. F., De Kloe, G. E., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
Structural Chemogenomics Databases to Navigate Protein-Ligand Interaction Space
Kanev, G. K., Kooistra, Albert J., 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 proceeding › Book chapter › Research › peer-review
Structural insights into serotonin receptor ligands polypharmacology
Podlewska, S., Kafel, R., Lacivita, E., Satała, G., Kooistra, Albert J., Vass, M., de Graaf, C., Leopoldo, M., Bojarski, A. J. & Mordalski, S., 10 May 2018, In: European Journal of Medicinal Chemistry. 151, p. 797-814 18 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Structure of the class D GPCR Ste2 dimer coupled to two G proteins
Velazhahan, V., Ma, N., Pándy-Szekeres, Gáspár, Kooistra, Albert J., Lee, Y., Gloriam, David E., Vaidehi, N. & Tate, C. G., 2021, In: Nature. 589, p. 148-153 +app 24 ppResearch output: Contribution to journal › Journal article › Research › peer-review
- Published
Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You?
Ballante, F., Kooistra, Albert J., Kampen, S., de Graaf, C. & Carlsson, J., 2021, In: Pharmacological Reviews. 73, 4, p. 527-565Research output: Contribution to journal › Review › Research › peer-review
Structure-based prediction of g-protein-coupled receptor ligand function: A β-adrenoceptor case study
Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
Structure-based virtual screening for fragment-like ligands of the G protein-coupled histamine H4 receptor
Istyastono, E. P., Istyastono, E. P., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review
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 J., 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 journal › Journal article › Research › peer-review
- Published
The G protein database, GproteinDb
Pándy-Szekeres, Gáspár, Esguerra, M., Hauser, Alexander Sebastian, Caroli, J., Munk, C., Pilger, S., Keseru, G. M., Kooistra, Albert J. & Gloriam, David E., 2022, In: Nucleic Acids Research. 50, D1, p. D518-D525Research output: Contribution to journal › Journal article › Research › peer-review
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 J., Nov 2019, In: Trends in Pharmacological Sciences. 40, 11, p. 818-832 15 p.Research output: Contribution to journal › Review › Research › peer-review
The Receptor Concept in 3D: From Hypothesis and Metaphor to GPCR–Ligand Structures
Kooistra, Albert J., de Graaf, C. & Timmerman, H., 1 Jan 2014, In: Neurochemical Research. 39, 10, p. 1850-1861 12 p.Research output: Contribution to journal › Review › Research › peer-review
ID: 196033213
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GPCRdb in 2021: integrating GPCR sequence, structure and function
Research output: Contribution to journal › Journal article › Research › peer-review
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The Landscape of Atypical and Eukaryotic Protein Kinases
Research output: Contribution to journal › Review › Research › peer-review
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KLIFS: an overhaul after the first 5 years of supporting kinase research
Research output: Contribution to journal › Journal article › Research › peer-review
Published