Zobrazeno 1 - 10
of 82
pro vyhledávání: '"Daan P Geerke"'
Autor:
Karla Frydenvang, Marlies C A Verkade-Vreeker, Floor Dohmen, Jan N M Commandeur, Maria Rafiq, Osman Mirza, Flemming Steen Jørgensen, Daan P Geerke
Publikováno v:
PLoS ONE, Vol 14, Iss 5, p e0217292 (2019)
The bacterial Cytochrome P450 (CYP) BM3 (CYP102A1) is one of the most active CYP isoforms. BM3 mutants can serve as a model for human drug-metabolizing CYPs and/or as biocatalyst for selective formation of drug metabolites. Hence, molecular and compu
Externí odkaz:
https://doaj.org/article/4ca0b68792244c2ca63e3d37d9ec192e
Autor:
Luigi Capoferri, Marlies C A Verkade-Vreeker, Danny Buitenhuis, Jan N M Commandeur, Manuel Pastor, Nico P E Vermeulen, Daan P Geerke
Publikováno v:
PLoS ONE, Vol 10, Iss 11, p e0142232 (2015)
Prediction of human Cytochrome P450 (CYP) binding affinities of small ligands, i.e., substrates and inhibitors, represents an important task for predicting drug-drug interactions. A quantitative assessment of the ligand binding affinity towards diffe
Externí odkaz:
https://doaj.org/article/3ed89fa3fa634a258200e17253a8f53b
Autor:
Stephanie Maiwald, Suthesh Sivapalaratnam, Mahdi M Motazacker, Julian C van Capelleveen, Ilze Bot, Saskia C de Jager, Miranda van Eck, Jennifer Jolley, Johan Kuiper, Jonathon Stephens, Cornelius A Albers, C Ruben Vosmeer, Heleen Kruize, Daan P Geerke, Allard C van der Wal, Chris M van der Loos, John J P Kastelein, Mieke D Trip, Willem H Ouwehand, Geesje M Dallinga-Thie, G Kees Hovingh
Publikováno v:
PLoS ONE, Vol 9, Iss 5, p e98289 (2014)
Genetic factors explain a proportion of the inter-individual variation in the risk for atherosclerotic events, but the genetic basis of atherosclerosis and atherothrombosis in families with Mendelian forms of premature atherosclerosis is incompletely
Externí odkaz:
https://doaj.org/article/d0ef6506d4f4491a80ea2afb192bac40
Autor:
Evan E. Bolton, Haralambos Sarimveis, Egon L. Willighagen, Hervé Ménager, Susanna-Assunta Sansone, Nina Jeliazkova, Antony J. Williams, Sirarat Sarntivijai, Emma L. Schymanski, Rob Stierum, Karel Berka, Pascal Kahlem, Jos Bessems, Pavel Babica, Montserrat Cases, Ludek Blaha, Hristo Aladjov, Reza Aalizadeh, Karine Audouze, Kasia Arturi, Alasdair Gray, Roland Grafström, Daan P. Geerke, Henner Hollert, Ola Spjuth, John M. Hancock, Kirtan Dave, Dimitrios Ε. Damalas, Thomas Exner, Marco Dilger, Boï Kone, Todor Kondic, Uko Maran, Steffen Neumann, Iseult Lynch, Fabien Jourdan, Philippe Rocca-Serra, Ferran Sanz, Danyel Jennen, Jos Kleinjans, Jana Klanova, Reza M. Salek, Sylvie Remy, Tobias Schulze, Brett Sallach, Penny Nymark, Sergio Martinez Cuesta, Noelia Ramirez, Herbert Oberacher, Craig E. Wheelock, Gerard J.P. van Westen, Barbara Zdrazil, Hilda Witters, Jonathan Tedds, Marvin Martens, Jaroslav Slobodnik, Ralf J.M. Weber, Nikolaos Thomaidis, Anže Županič, Chris T. Evelo
Publikováno v:
F1000Research, Vol 10 (2023)
Toxicology has been an active research field for many decades, with academic, industrial and government involvement. Modern omics and computational approaches are changing the field, from merely disease-specific observational models into target-speci
Externí odkaz:
https://doaj.org/article/e59322df245a4fc28be0854e2252ef78
Autor:
Minglong Liu, Ryoji Yoshisada, Avand Amedi, Antonius J. P. Hopstaken, Mirte N. Pascha, Cornelis A. M. de Haan, Daan P. Geerke, David A. Poole, Seino A. K. Jongkees
Publikováno v:
Liu, M, Yoshisada, R, Amedi, A, Hopstaken, A J P, Pascha, M N, de Haan, C A M, Geerke, D P, Poole, D A & Jongkees, S A K 2023, ' An Efficient, Site-Selective and Spontaneous Peptide Macrocyclisation During in vitro Translation ', Chemistry-A European Journal, vol. 29, no. 14, e202203923, pp. 1-9 . https://doi.org/10.1002/chem.202203923
Chemistry-A European Journal, 29(14):e202203923, 1-9. Wiley-VCH Verlag
Chemistry-A European Journal, 29(14):e202203923, 1-9. Wiley-VCH Verlag
Macrocyclisation provides a means of stabilising the conformation of peptides, often resulting in improved stability, selectivity, affinity, and cell permeability. In this work we report a new approach to peptide macrocyclisation using a cyanobenzoth
Autor:
Ida de Vries, Danique Ammerlaan, Tatjana Heidebrecht, Patrick H. N. Celie, Daan P. Geerke, Robbie P. Joosten, Anastassis Perrakis
Base-J (β-D-Glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J Binding Protein 1 (JBP1), that has a thymidine hydroxy
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0b4785f11a61fea515b902704d2b573e
https://doi.org/10.1101/2023.01.23.525147
https://doi.org/10.1101/2023.01.23.525147
Autor:
Felix M. Paulussen, Gina K. Schouten, Carolin Moertl, Jolanda Verheul, Irma Hoekstra, Gregory M. Koningstein, George H. Hutchins, Aslihan Alkir, Rosa A. Luirink, Daan P. Geerke, Peter van Ulsen, Tanneke den Blaauwen, Joen Luirink, Tom N. Grossmann
Publikováno v:
Journal of the American Chemical Society. 144(33)
The use of antibiotics is threatened by the emergence and spread of multidrug-resistant strains of bacteria. Thus, there is a need to develop antibiotics that address new targets. In this respect, the bacterial divisome, a multi-protein complex centr
Autor:
Thomas Hansen, Xiaobo Sun, Marco Dalla Tiezza, Willem‐Jan van Zeist, Joost N. P. van Stralen, Daan P. Geerke, Lando P. Wolters, Jordi Poater, Trevor A. Hamlin, F. Matthias Bickelhaupt
Publikováno v:
Chemistry-A European Journal, 28(44):e202201093. Wiley-VCH Verlag
Chemistry : a European Journal, 28, 44, pp. 1-11
Chemistry : a European Journal, 28, 1-11
Hansen, T, Sun, X, Dalla Tiezza, M, van Zeist, W J, van Stralen, J N P, Geerke, D P, Wolters, L P, Poater, J, Hamlin, T A & Bickelhaupt, F M 2022, ' C−X Bond Activation by Palladium : Steric Shielding versus Steric Attraction ', Chemistry-A European Journal, vol. 28, no. 44, e202201093 . https://doi.org/10.1002/chem.202201093
Chemistry : a European Journal, 28, 44, pp. 1-11
Chemistry : a European Journal, 28, 1-11
Hansen, T, Sun, X, Dalla Tiezza, M, van Zeist, W J, van Stralen, J N P, Geerke, D P, Wolters, L P, Poater, J, Hamlin, T A & Bickelhaupt, F M 2022, ' C−X Bond Activation by Palladium : Steric Shielding versus Steric Attraction ', Chemistry-A European Journal, vol. 28, no. 44, e202201093 . https://doi.org/10.1002/chem.202201093
The C−X bond activation (X = H, C) of a series of substituted C(n°)−H and C(n°)−C(m°) bonds with C(n°) and C(m°) = H3C− (methyl, 0°), CH3H2C− (primary, 1°), (CH3)2HC− (secondary, 2°), (CH3)3C− (tertiary, 3°) by palladium were i
Publikováno v:
ChemBioChem, 21(10), 1461-1472. Wiley-VCH Verlag
Chembiochem
Luirink, R A, Verkade-Vreeker, M C A, Commandeur, J N M & Geerke, D P 2020, ' A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450-Catalyzed Substrate Conversion ', ChemBioChem, vol. 21, no. 10, pp. 1461-1472 . https://doi.org/10.1002/cbic.201900751
Chembiochem
Luirink, R A, Verkade-Vreeker, M C A, Commandeur, J N M & Geerke, D P 2020, ' A Modified Arrhenius Approach to Thermodynamically Study Regioselectivity in Cytochrome P450-Catalyzed Substrate Conversion ', ChemBioChem, vol. 21, no. 10, pp. 1461-1472 . https://doi.org/10.1002/cbic.201900751
The regio‐ (and stereo‐)selectivity and specific activity of cytochrome P450s are determined by the accessibility of potential sites of metabolism (SOMs) of the bound substrate relative to the heme, and the activation barrier of the regioselectiv
Publikováno v:
Journal of Chemical Theory and Computation
Rifai, E A, Ferrario, V, Pleiss, J & Geerke, D P 2020, ' Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation ', Journal of chemical theory and computation, vol. 16, no. 2, pp. 1300-1310 . https://doi.org/10.1021/acs.jctc.9b00890
Journal of chemical theory and computation, 16(2), 1300-1310. American Chemical Society
Rifai, E A, Ferrario, V, Pleiss, J & Geerke, D P 2020, ' Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation ', Journal of chemical theory and computation, vol. 16, no. 2, pp. 1300-1310 . https://doi.org/10.1021/acs.jctc.9b00890
Journal of chemical theory and computation, 16(2), 1300-1310. American Chemical Society
Calculating free energies of binding (ΔGbind) between ligands and their target protein is of major interest to drug discovery and safety, yet it is still associated with several challenges and difficulties. Linear interaction energy (LIE) is an effi