Albert Jelke Kooistra

Publikation

Publikationer pr. år 2010 2013 2014 2015 2016 2017 2018 2019

• 23 Tidsskriftartikel
• 5 Bidrag til bog/antologi
• 5 Review

Publikationer pr. år

Publikationer pr. år

Søgeresultater

• 2019

  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., 25 apr. 2019, I: Journal of Medicinal Chemistry. 62, 8, s. 3784-3839 56 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • G-Protein-Coupled Receptors 100%
  • Mutation 84%
  • Ligands 70%
  • Ligand 43%
  • G-protein-coupled receptor 34 31%
  13 Citationer (Scopus)
• 2018

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

  Kooistra, A. J., Vass, M., McGuire, R., Leurs, R., de Esch, I. J. P., Vriend, G., Verhoeven, S. & de Graaf, C., 20 mar. 2018, I: ChemMedChem. 13, 6, s. 614-626 13 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Cheminformatics 100%
  • Workflow 67%
  • Drug Discovery 63%
  • Ligands 43%
  • Drug 32%
  9 Citationer (Scopus)

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

  Vass, M., Kooistra, A. J., Verhoeven, S., Gloriam, D., de Esch, I. J. P. & de Graaf, C., 1 jan. 2018, Methods in Molecular Biology. Humana Press, s. 73-113 41 s. (Methods in Molecular Biology, Bind 1705).

  Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › peer review

  • G-Protein-Coupled Receptors 100%
  • Binding Sites 38%
  • Ligands 35%
  • Workflow 27%
  • Mutation 13%
  4 Citationer (Scopus)

• Chemical Diversity in the G Protein-Coupled Receptor Superfamily

  Vass, M., Kooistra, A. J., Yang, D., Stevens, R. C., Wang, M. W. & de Graaf, C., 1 maj 2018, I: Trends in Pharmacological Sciences. 39, 5, s. 494-512 19 s.

  Publikation: Bidrag til tidsskrift › Review › peer review

  • G-Protein-Coupled Receptors 100%
  • Ligands 70%
  • Ligand 43%
  • Cheminformatics 26%
  • Pharmacological Property 19%
  34 Citationer (Scopus)

• 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, A. J., De Graaf, C., Vischer, H. F., Leurs, R., Briddon, S. J., Kellam, B. & Hill, S. J., 1 dec. 2018, I: Scientific Reports. 8, 1, 1572.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Histamine H1 Antagonists 100%
  • Histamine H1 Receptors 90%
  • Kinetics 50%
  • Ligands 49%
  • Pyrilamine 38%
  35 Citationer (Scopus)

• Structural insights into serotonin receptor ligands polypharmacology

  Podlewska, S., Kafel, R., Lacivita, E., Satała, G., Kooistra, A. J., Vass, M., de Graaf, C., Leopoldo, M., Bojarski, A. J. & Mordalski, S., 10 maj 2018, I: European Journal of Medicinal Chemistry. 151, s. 797-814 18 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Polypharmacology 100%
  • Serotonin Receptors 69%
  • Serotonin 66%
  • serotonin 7 receptor 55%
  • Ligands 42%
  6 Citationer (Scopus)

• 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, A. 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, I: Journal of the American Chemical Society. 140, 12, s. 4232-4243 12 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Histamine H3 Receptors 100%
  • Ligands 88%
  • G-Protein-Coupled Receptors 67%
  • Antagonist 62%
  • Proteins 61%
  25 Citationer (Scopus)
• 2017

  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, A. J., Ritschel, T. & De Graaf, C., 27 feb. 2017, I: Journal of Chemical Information and Modeling. 57, 2, s. 115-121 7 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Ligands 100%
  • Virtual machine 76%
  • Proteins 68%
  • workflow 54%
  • infrastructure 52%
  18 Citationer (Scopus)

• Kinase-Centric Computational Drug Development

  Kooistra, A. J. & Volkamer, A., 1 jan. 2017, Annual Reports in Medicinal Chemistry. Academic Press, s. 263-299 37 s. (Annual Reports in Medicinal Chemistry, Bind 50).

  Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › peer review

  • Bioactivity 100%
  • Phosphotransferase Inhibitor 87%
  • Drug Target 79%
  • Drug 73%
  • Disorder 59%
  17 Citationer (Scopus)

• Structural Chemogenomics Databases to Navigate Protein-Ligand Interaction Space

  Kanev, G. K., Kooistra, A. J., de Esch, I. J. P. & de Graaf, C., 3 jun. 2017, The Future of Drug Discovery. Elsevier Science Inc., Bind 1-8. s. 444-471 28 s.

  Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › peer review

  • Ligands 100%
  • Proteins 68%
  • Data curation 18%
  • Bioactivity 14%
  • Molecules 10%
  2 Citationer (Scopus)
• 2016

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

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

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • G-Protein-Coupled Receptors 100%
  • Research Design 78%
  • Ligands 70%
  • Histamine H1 Receptors 64%
  • Protein Binding 49%
  51 Citationer (Scopus)

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

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

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Histamine H1 Receptors 100%
  • Histamine 86%
  • Amines 80%
  • Tertiary Amine 79%
  • Piperidine 77%
  19 Citationer (Scopus)

• KLIFS: A structural kinase-ligand interaction database

  Kooistra, A. J., Kanev, G. K., Van Linden, O. P. J., Leurs, R., De Esch, I. J. P. & De Graaf, C., 1 jan. 2016, I: Nucleic Acids Research. 44, D1, s. D365-D371

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Phosphotransferases 100%
  • Ligands 91%
  • Databases 77%
  • Dermatoglyphics 60%
  • Protein Kinases 47%
  81 Citationer (Scopus)

• Molecular interaction fingerprint approaches for GPCR drug discovery

  Vass, M., Kooistra, A. J., Ritschel, T., Leurs, R., de Esch, I. JP. & de Graaf, C., 1 okt. 2016, I: Current Opinion in Pharmacology. 30, s. 59-68 10 s.

  Publikation: Bidrag til tidsskrift › Review › peer review

  • Dermatoglyphics 100%
  • Drug Discovery 87%
  • G-Protein-Coupled Receptors 85%
  • Drug 45%
  • Binding Site 40%
  28 Citationer (Scopus)

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

  Jansen, C., Kooistra, A. J., Kanev, G. K., Leurs, R., De Esch, I. J. P. & De Graaf, C., 11 aug. 2016, I: Journal of Medicinal Chemistry. 59, 15, s. 7029-7065 37 s.

  Publikation: Bidrag til tidsskrift › Review › peer review

  • Phosphoric Diester Hydrolases 100%
  • Drug Design 98%
  • Ligands 60%
  • Databases 51%
  • Drug 45%
  36 Citationer (Scopus)
• 2015

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

  Méndez-Lucio, O., Kooistra, A. J., Graaf, C. D., Bender, A. & Medina-Franco, J. L., 23 feb. 2015, I: Journal of Chemical Information and Modeling. 55, 2, s. 251-262 12 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Ligands 100%
  • Proteins 68%
  • interaction 35%
  • Ligand 33%
  • activity structure 11%
  19 Citationer (Scopus)

• 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, A. J., Vischer, H. F., Nijmeijer, S., Haaksma, E. E. J., Leurs, R., De Esch, I. J. P. & De Graaf, C., 26 maj 2015, I: Journal of Chemical Information and Modeling. 55, 5, s. 1030-1034 5 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Ligands 100%
  • Histamine 85%
  • Serotonin 83%
  • Screening 70%
  • Fusion reactions 60%
  13 Citationer (Scopus)

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

  Kooistra, A. J., Leurs, R., De Esch, I. J. P. & De Graaf, C., 26 maj 2015, I: Journal of Chemical Information and Modeling. 55, 5, s. 1045-1061 17 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Ligands 100%
  • Agonist 72%
  • Proteins 68%
  • Inverse Agonist 61%
  • Antagonist 60%
  32 Citationer (Scopus)

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

  Istyastono, E. P., Istyastono, E. P., Kooistra, A. 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, I: MedChemComm. 6, 6, s. 1003-1017 15 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Histamine H4 Receptors 100%
  • Histamine 67%
  • GTP-Binding Proteins 60%
  • Ligands 42%
  • Adrenergic 31%
  37 Citationer (Scopus)

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

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

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • G Protein 100%
  • Arrestins 98%
  • arrestins 94%
  • trafficking 84%
  • chemokines 79%
  13 Citationer (Scopus)
• 2014

  From three-dimensional GPCR structure to rational ligand discovery

  Kooistra, A. 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, s. 129-157 29 s. (Advances in Experimental Medicine and Biology, Bind 796).

  Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › peer review

  • Ligands 100%
  • Structural Models 20%
  • Workflow 19%
  • G-Protein-Coupled Receptors 17%
  • Proteins 6%
  31 Citationer (Scopus)

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

  Van Linden, O. P. J., Kooistra, A. J., Leurs, R., De Esch, I. J. P. & De Graaf, C., 23 jan. 2014, I: Journal of Medicinal Chemistry. 57, 2, s. 249-277 29 s.

  Publikation: Bidrag til tidsskrift › Review › peer review

  • Dermatoglyphics 100%
  • Phosphotransferases 66%
  • Ligands 60%
  • Databases 51%
  • Designer Drug 42%
  155 Citationer (Scopus)

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

  Kooistra, A. J., de Graaf, C. & Timmerman, H., 1 jan. 2014, I: Neurochemical Research. 39, 10, s. 1850-1861 12 s.

  Publikation: Bidrag til tidsskrift › Review › peer review

  • Metaphor 100%
  • G-Protein-Coupled Receptors 72%
  • Binding Site 50%
  • Chemistry 41%
  • Crystal Structure 35%
  7 Citationer (Scopus)
• 2013

  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., 1 sep. 2013, I: British Journal of Pharmacology. 170, 1, s. 101-126 26 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Histamine Receptors 100%
  • G-Protein-Coupled Receptors 75%
  • Ligands 53%
  • Binding Sites 13%
  • Protein Sequence Analysis 6%
  58 Citationer (Scopus)

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

  Jansen, C., Wang, H., Kooistra, A. 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, I: Journal of Medicinal Chemistry. 56, 5, s. 2087-2096 10 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Trypanosoma brucei PDEB1 protein 100%
  • Cyclic Nucleotide 52%
  • Trypanosoma brucei brucei 52%
  • Phosphodiesterase Inhibitors 48%
  • Cyclic Nucleotides 48%
  45 Citationer (Scopus)

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

  Kooistra, A. 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. s. 279-336 58 s. (Methods in Enzymology, Bind 522).

  Publikation: Bidrag til bog/antologi/rapport › Bidrag til bog/antologi › Forskning › peer review

  • G-Protein-Coupled Receptors 100%
  • Ligands 70%
  • Structural Models 39%
  • Sequence Alignment 20%
  • Workflow 18%
  48 Citationer (Scopus)

• Mapping histamine H₄ receptor-ligand binding modes

  Schultes, S., Nijmeijer, S., Engelhardt, H., Kooistra, A. J., Vischer, H. F., De Esch, I. J. P., Haaksma, E. E. J., Leurs, R. & De Graaf, C., 1 jan. 2013, I: MedChemComm. 4, 1, s. 193-204 12 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Histamine H4 Receptors 100%
  • Histamine 67%
  • Ligands 42%
  • Ligand 26%
  • Structure-Activity Relationship 25%
  30 Citationer (Scopus)

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

  De Graaf, C., Vischer, H. F., De Kloe, G. E., Kooistra, A. 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, I: Drug Discovery Today. 18, 7-8, s. 323-330 8 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Ligands 100%
  • Ligand-Gated Ion Channels 64%
  • Chemical Entity 60%
  • Protein 58%
  • Proteins 52%
  25 Citationer (Scopus)
• 2012

  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, A. J., De Graaf, C. & De Esch, I. J. P., 1 okt. 2012, I: Bioorganic and Medicinal Chemistry. 20, 19, s. 5992-6002 11 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Nicotinic Receptors 100%
  • Computer Simulation 85%
  • epibatidine 72%
  • Epibatidine 71%
  • -Log Ki 68%
  11 Citationer (Scopus)

• 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, A. J., Nijmeijer, S., Kuijer, M., Wijtmans, M., Mannhold, R., Leurs, R., De Esch, I. J. P. & De Graaf, C., 21 dec. 2012, I: Journal of Chemical Information and Modeling. 52, 12, s. 3308-3324 17 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Ligands 100%
  • Histamine 85%
  • Molecules 73%
  • Screening 70%
  • Proteins 68%
  64 Citationer (Scopus)
• 2011

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

  De Graaf, C., Kooistra, A. 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, I: Journal of Medicinal Chemistry. 54, 23, s. 8195-8206 12 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Histamine 100%
  • G-Protein-Coupled Receptors 66%
  • Ligands 62%
  • Computer Simulation 41%
  • Ligand 38%
  173 Citationer (Scopus)

• 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, A. J., Vischer, H. F., De Esch, I. J. P., Leurs, R. & De Graaf, C., 8 dec. 2011, I: Journal of Medicinal Chemistry. 54, 23, s. 8136-8147 12 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Clobenpropit 100%
  • Quantitative Structure-Activity Relationship 67%
  • Histamine 55%
  • QSAR Study 50%
  • Mutagenesis 48%
  50 Citationer (Scopus)
• 2010

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

  Kooistra, A. J., Binsl, T. W., Van Beek, J. H. G. M., De Graaf, C. & Heringa, J., 25 okt. 2010, I: Journal of Chemical Information and Modeling. 50, 10, s. 1772-1780 9 s.

  Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

  • Carrier concentration 100%
  • Screening 65%
  • Electron Density 64%
  • Ligands 26%
  • Molecules 19%
  8 Citationer (Scopus)