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Development of a mixed quantum mechanical/molecular mechanical method and its application to biochemical systems
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List of publications |
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Andrea Scarpino, László Petri, Damijan Knez, Tímea Imre, Péter Ábrányi-Balogh, György G. Ferenczy, Stanislav Gobec, György M. Keserű: WIDOCK: A Warhead-Independent Virtual Screening Protocol for Cysteine Targeted Covalent Inhibitors, JOURNAL OF CHEMICAL INFORMATION AND MODELING in revision, 2020 | Enrico Margiotta, Stephanie C. C. van der Lubbe, Lucas de Azevedo Santos, Gabor Paragi, Stefano Moro, F. Matthias Bickelhaupt and Célia Fonseca Guerra: Halogen Bonds in Ligand-Protein Systems: Molecular Orbital Theory for Drug Design, JOURNAL OF CHEMICAL INFORMATION AND MODELING in revision, 2020 | Kiss, Dóra Judit, Menyhárd, Dóra.K., Oláh, J., Tóth, G., Stirling, A., Ferenczy, György G.: The reaction pathway of pseudouridylation by box H/ACA pseudouridine synthase: Insight from quantum mechanical/molecular mechanical free energy calculations, MANUSCRIPT IN PREPARATION, 2020 | J. Gera, G. Ferencz, Z. Kupihar, L. Kovacs, G. Paragi: Ionmobility in natural and artificial quadruplex structures, MANUSCRIPT IN PREPARATION, 2020 | Bence Hégely, Ferenc Bogár, György G. Ferenczy, Mihály Kállay: A QM/MM program using frozen localized orbitals and the Huzinaga equation, Theor. Chem. Acc., 2015 | Dóra Judit Kiss, Julianna Oláh, Gergely Tóth, Csaba Magyar, Dóra Karancsiné Menyhárd, György G. Ferenczy: Computational study of the reaction mechanism of uridine isomerisation by box H/ACA pseudouridine synthase, Athene's Chemistry Conference, Budapest, Book of Abstract, 2015 | Bence Hégely, Péter R. Nagy, György G. Ferenczy, Mihály Kállay: Exact density functional and wave function embedding schemes based on orbital localization, The Journal of Chemical Physics, 2016 | D. J. Kiss, J. Oláh, G. Tóth, Cs. Magyar, D. Karancsiné Menyhárd, G. G. Ferenczy: Computational study of the reaction mechanism of the box H/ACA pseudouridine synthase catalysed uridine isomerisation, Book of Abstracts 16th International Conference on Theoretical Aspects of Catalysis Zakopane, Poland June 19-23, 2016, ISBN 978-83-60514-25-2, 2016 | Kiss Dóra Judit, Oláh Julianna, Tóth Gergely, Magyar Csaba, Karancsiné Menyhárd Dóra, Ferenczy György: Pszeudouridináz katalizált uridin izomerizáció mechanizmusának vizsgálata kvantumkémiai módszerekkel, http://tab.mta.hu/miskolci-teruleti-bizottsag/esemenyek/kemomoqsar-2016-szimpozium, 2016 | Bence Hégely, Péter R. Nagy, György G. Ferenczy, Mihály Kállay: Exact density functional and wave function embedding schemes based on orbital localization, Book of Abstracts International Symposium of Theoretical and Chemical Physics (ISTCP), Grand Forks, North Dakota, USA, 2016 | D. J. Kiss, J. Oláh, G. Tóth, D. K. Menyhárd, G. G. Ferenczy: QM/MM study of the reaction mechanism of the box H/ACA pseudouridine synthase catalysed uridine isomerisation, http://www.watoc2017.com/files/WATOC17/Downloads/WATOC17_Poster-Session2.pdf, 2017 | György G. Ferenczy: Hybrid quantum mechamics/molecular mechanics (QM/MM) method development and application to biochemical systems, Book of Abstracts 15th Central European Symposium on Theoretical Chemistry, Wisla, Poland, September 3-6, 2017 | Zoltán Orgován, György G. Ferenczy, Thomas Steinbrecher, Bence Szilágyi, Dávid Bajusz, György M. Keserű: Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors, Journal of Computer-Aided Molecular Design, 2018 | Dóra J. Kiss Julianna Oláh Gergely Tóth Dóra K. Menyhárd György G. Ferenczy: Quantum chemical calculations support pseudouridine synthase reaction through a glycal intermediate and provide details of the mechanism, Theoretical Chemistry Accounts, 2018 | J. Gera, T. Szögi, Zs. Bozsó, L. Fülöp, E. E. Barrera, A. M. Rodriguez, L. Méndez, C.M.L. Delpiccolo, E. G. Mata, F. Cioffi, K. Broersen, G. Paragi, R.D. Enriz: Searching for improved mimetic peptides inhibitors preventing conformational transition of amyloid-β42 monomer, BIOORGANIC CHEMISTRY, 2018 | Levente M. Mihalovits, György G. Ferenczy, György M. Keserű: Catalytic Mechanism and Covalent Inhibition of UDP‑N‑Acetylglucosamine Enolpyruvyl Transferase (MurA): Implications to the Design of Novel Antibacterials, Journal of Chemical Information and Modeling, 2019 | Dóra Judit Kiss, György G. Ferenczy: A detailed mechanism of the oxidative half-reaction of D-amino acid oxidase: another route for flavin oxidation, Organic & Biomolecular Chemistry, 2019 |
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