Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane
Stroet, Martin, Caron, Bertrand, Visscher, Koen M, Geerke, Daan P, Malde, Alpeshkumar K, Mark, Alan E
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Published in Journal of chemical theory and computation (13.11.2018)
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Inakollu, VS Sandeep, Geerke, Daan P, Rowley, Christopher N, Yu, Haibo
Published in Current opinion in structural biology (01.04.2020)
Published in Current opinion in structural biology (01.04.2020)
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A QM/MM Derived Polarizable Water Model for Molecular Simulation
Visscher, Koen M, Swope, William C, Geerke, Daan P
Published in Molecules (Basel, Switzerland) (29.11.2018)
Published in Molecules (Basel, Switzerland) (29.11.2018)
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Structural analysis of Cytochrome P450 BM3 mutant M11 in complex with dithiothreitol
Frydenvang, Karla, Verkade-Vreeker, Marlies C A, Dohmen, Floor, Commandeur, Jan N M, Rafiq, Maria, Mirza, Osman, Jørgensen, Flemming Steen, Geerke, Daan P
Published in PloS one (24.05.2019)
Published in PloS one (24.05.2019)
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Covalent Proteomimetic Inhibitor of the Bacterial FtsQB Divisome Complex
Paulussen, Felix M., Schouten, Gina K., Moertl, Carolin, Verheul, Jolanda, Hoekstra, Irma, Koningstein, Gregory M., Hutchins, George H., Alkir, Aslihan, Luirink, Rosa A., Geerke, Daan P., van Ulsen, Peter, den Blaauwen, Tanneke, Luirink, Joen, Grossmann, Tom N.
Published in Journal of the American Chemical Society (24.08.2022)
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Engineered factor Xa variants retain procoagulant activity independent of direct factor Xa inhibitors
Verhoef, Daniël, Visscher, Koen M, Vosmeer, C Ruben, Cheung, Ka Lei, Reitsma, Pieter H, Geerke, Daan P, Bos, Mettine H A
Published in Nature communications (13.09.2017)
Published in Nature communications (13.09.2017)
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Charge group partitioning in biomolecular simulation
Canzar, Stefan, El-Kebir, Mohammed, Pool, René, Elbassioni, Khaled, Mark, Alan E, Geerke, Daan P, Stougie, Leen, Klau, Gunnar W
Published in Journal of computational biology (01.03.2013)
Published in Journal of computational biology (01.03.2013)
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The Role of c-Met as a Biomarker and Player in Innate and Acquired Resistance in Non-Small-Cell Lung Cancer: Two New Mutations Warrant Further Studies
Van Der Steen, Nele, Zwaenepoel, Karen, Mazzaschi, Giulia, A Luirink, Rosa, P Geerke, Daan, Op de Beeck, Ken, Hermans, Christophe, Tiseo, Marcello, Van Schil, Paul, Lardon, Filip, Germonpré, Paul, Rolfo, Christian, Giovannetti, Elisa, J Peters, Godefridus, Pauwels, Patrick
Published in Molecules (Basel, Switzerland) (04.12.2019)
Published in Molecules (Basel, Switzerland) (04.12.2019)
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OFraMP: a fragment-based tool to facilitate the parametrization of large molecules
Stroet, Martin, Caron, Bertrand, Engler, Martin S., van der Woning, Jimi, Kauffmann, Aude, van Dijk, Marc, El-Kebir, Mohammed, Visscher, Koen M., Holownia, Josef, Macfarlane, Callum, Bennion, Brian J., Gelpi-Dominguez, Svetlana, Lightstone, Felice C., van der Storm, Tijs, Geerke, Daan P., Mark, Alan E., Klau, Gunnar W.
Published in Journal of computer-aided molecular design (01.08.2023)
Published in Journal of computer-aided molecular design (01.08.2023)
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Biomolecular Modeling: Goals, Problems, Perspectives
van Gunsteren, Wilfred F., Bakowies, Dirk, Baron, Riccardo, Chandrasekhar, Indira, Christen, Markus, Daura, Xavier, Gee, Peter, Geerke, Daan P., Glättli, Alice, Hünenberger, Philippe H., Kastenholz, Mika A., Oostenbrink, Chris, Schenk, Merijn, Trzesniak, Daniel, van der Vegt, Nico F. A., Yu, Haibo B.
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Published in Angewandte Chemie (International ed.) (19.06.2006)
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An anti-tuberculosis compound screen using a zebrafish infection model identifies an aspartyl-tRNA synthetase inhibitor
Habjan, Eva, Ho, Vien Q T, Gallant, James, van Stempvoort, Gunny, Jim, Kin Ki, Kuijl, Coen, Geerke, Daan P, Bitter, Wilbert, Speer, Alexander
Published in Disease models & mechanisms (01.12.2021)
Published in Disease models & mechanisms (01.12.2021)
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The GROMOS software for biomolecular simulation: GROMOS05
Christen, Markus, Hünenberger, Philippe H., Bakowies, Dirk, Baron, Riccardo, Bürgi, Roland, Geerke, Daan P., Heinz, Tim N., Kastenholz, Mika A., Kräutler, Vincent, Oostenbrink, Chris, Peter, Christine, Trzesniak, Daniel, van Gunsteren, Wilfred F.
Published in Journal of computational chemistry (01.12.2005)
Published in Journal of computational chemistry (01.12.2005)
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Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation
Capoferri, Luigi, Verkade-Vreeker, Marlies C A, Buitenhuis, Danny, Commandeur, Jan N M, Pastor, Manuel, Vermeulen, Nico P E, Geerke, Daan P
Published in PloS one (09.11.2015)
Published in PloS one (09.11.2015)
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C−X Bond Activation by Palladium: Steric Shielding versus Steric Attraction
Hansen, Thomas, Sun, Xiaobo, Dalla Tiezza, Marco, Zeist, Willem‐Jan, Stralen, Joost N. P., Geerke, Daan P., Wolters, Lando P., Poater, Jordi, Hamlin, Trevor A., Bickelhaupt, F. Matthias
Published in Chemistry : a European journal (04.08.2022)
Published in Chemistry : a European journal (04.08.2022)
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Genetic Control and Evolution of Anthocyanin Methylation
Provenzano, Sofia, Spelt, Cornells, Hosokawa, Satoko, Nakamura, Noriko, Brugliera, Filippa, Demelis, Linda, Geerke, Daan P., Schubert, Andrea, Tanaka, Yoshikazu, Quattrocchio, Francesca, Koes, Ronald
Published in Plant physiology (Bethesda) (01.07.2014)
Published in Plant physiology (Bethesda) (01.07.2014)
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