Albert J. Kooistra

Albert J. Kooistra

Associate Professor

ORCID: 0000-0001-5514-6021

Publication year:
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1 - 25 out of 53Page size: 25
  1. 2010

  2. 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

  3. 2011

  4. 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

  5. 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

  6. 2012

  7. 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

  8. 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 J., 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 journal › Journal article › Research › peer-review

  9. 2013

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 2014

  16. 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

  17. 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

  18. 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

  19. 2015

  20. 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

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

    De Munnik, S. M., Kooistra, Albert J., 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 journal › Journal article › Research › peer-review

  22. 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

  23. 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

  24. 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

  25. 2016

  26. 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-D371

    Research output: Contribution to journal › Journal article › Research › peer-review

  27. 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

  28. 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

  29. 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

  30. 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

  31. 2017

  32. 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

  33. 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

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