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SAR and QSAR in Environmental Research Volume 19, 2008 - Issue 1-2
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Original Articles

Molecular dynamics simulations of the enzyme Catechol-O-Methyltransferase: methodological issuesFootnote1

A Bunker Drug Discovery and Development Technology Center, Faculty of Pharmacy, University of Helsinki, FinlandCorrespondence[email protected]
,
PT Männistö Division of Pharmacology and Toxicology, Faculty of Pharmacy, University of Helsinki Finland, Québec, Canada
,
J.-F. St. Pierre Division of Pharmacology and Toxicology, Faculty of Pharmacy, University of Helsinki Finland, Québec, Canada; Département de Physique and Regroupement Québécois sur les Matériaux de Pointe, Université de Montréal Montreal, Québec, Canada
,
T Róg Laboratory of Physics, Helsinki University of Technology Finland, Kraków, Poland; Department of Biophysics, Faculty of Biotechnology, Jagiellonian University, Kraków, Poland
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P Pomorski Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
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L Stimson Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
&
M Karttunen Department of Biophysics, Faculty of Biotechnology, Jagiellonian University, Kraków, Poland; Department of Applied Mathematics, The University of Western Ontario, London, Ontario, Canada
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Pages 179-189 | Received 05 Sep 2007, Accepted 26 Nov 2007, Published online: 04 Dec 2010

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Hunday Govindasamy, Sivanandam Magudeeswaran & Kumaradhas Poomani. (2020) Identification of novel flavonoid inhibitor of Catechol-O-Methyltransferase enzyme by molecular screening, quantum mechanics/molecular mechanics and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics 38:18, pages 5307-5319.
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L.F. Wang, Y. Wang, Z.Y. Yang, J. Zhao, H.B. Sun & S.L. Wu. (2020) Revealing binding selectivity of inhibitors toward bromodomain-containing proteins 2 and 4 using multiple short molecular dynamics simulations and free energy analyses. SAR and QSAR in Environmental Research 31:5, pages 373-398.
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Y. Wang, L.F. Wang, L.L. Zhang, H.B. Sun & J. Zhao. (2020) Molecular mechanism of inhibitor bindings to bromodomain-containing protein 9 explored based on molecular dynamics simulations and calculations of binding free energies. SAR and QSAR in Environmental Research 31:2, pages 149-170.
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K. Kaszuba, T. Róg, J.-F. St. Pierre, P.T. Männistö, M. Karttunen & A. Bunker. (2009) Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity. SAR and QSAR in Environmental Research 20:7-8, pages 595-609.
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Articles from other publishers (7)

Kerlen T. Korbeld & Maximilian J. L. J. Fürst. (2023) Curse and Blessing of Non‐Proteinogenic Parts in Computational Enzyme Engineering. ChemBioChem 24:12.
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Subodh Kamble, Sagar Barale, Maruti Dhanavade & Kailas Sonawane. (2021) Structural significance of Neprylysin from Streptococcus suis GZ1 in the degradation of Aβ peptides, a causative agent in Alzheimer's disease. Computers in Biology and Medicine 136, pages 104691.
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Pedro Bastos, Tiago Gomes & Laura Ribeiro. 2017. Reviews of Physiology, Biochemistry and Pharmacology, Vol. 173. Reviews of Physiology, Biochemistry and Pharmacology, Vol. 173 1 39 .
Karol Kaszuba, Tomasz Róg, Reinis Danne, Peter Canning, Vilmos Fülöp, Tünde Juhász, Zoltán Szeltner, J.-F. St. Pierre, Arturo García-Horsman, Pekka T. Männistö, Mikko Karttunen, Jyrki Hokkanen & Alex Bunker. (2012) Molecular dynamics, crystallography and mutagenesis studies on the substrate gating mechanism of prolyl oligopeptidase. Biochimie 94:6, pages 1398-1411.
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Adam Orłowski, Jean-François St-Pierre, Aniket Magarkar, Alex Bunker, Marta Pasenkiewicz-Gierula, Ilpo Vattulainen & Tomasz Róg. (2011) Properties of the Membrane Binding Component of Catechol- O -methyltransferase Revealed by Atomistic Molecular Dynamics Simulations . The Journal of Physical Chemistry B 115:46, pages 13541-13550.
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Karol Kaszuba, Tomasz Róg, Krzysztof Bryl, Ilpo Vattulainen & Mikko Karttunen. (2010) Molecular Dynamics Simulations Reveal Fundamental Role of Water As Factor Determining Affinity of Binding of β-Blocker Nebivolol to β 2 -Adrenergic Receptor . The Journal of Physical Chemistry B 114:25, pages 8374-8386.
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Eiichi Tsuji, Kosuke Okazaki, Masayuki Isaji & Kei Takeda. (2009) Crystal structures of the Apo and Holo form of rat catechol-O-methyltransferase. Journal of Structural Biology 165:3, pages 133-139.
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