Výpis publikací

LAPČÍK, Petr, R. Greg STACEY, David POTĚŠIL, Petr KULHÁNEK, Leonard J. FOSTER a Pavel BOUCHAL. Global interactome mapping reveals pro-tumorigenic interactions of NF-κB in breast cancer. Molecular and Cellular Proteomics. Elsevier, 2024. ISSN 1535-9484. Dostupné z: https://dx.doi.org/10.1016/j.mcpro.2024.100744.

ZEMANÍK, Július a Petr KULHÁNEK. QM/MM Reaction Simulations of Alpha-(1,3)-fucosyltransferase of Helicobacter pylori. In XX Discussions in Structural Molecular Biology and 7th User Meeting of CIISB. 2024. ISSN 1211-5894.

ZEMANÍK, Július a Petr KULHÁNEK. Structure of the Pre-reaction Complex of Alpha-(1,3)-fucosyltransferase of Helicobacter pylori. In XXII. Meeting of Biochemists and Molecular Biologists. 2023. ISBN 978-80-280-0409-5.

ZEMANÍK, Július a Petr KULHÁNEK. Structure of the Pre-reaction Complex of FucT. In XIX Discussions in Structural Molecular Biology and 6th User Meeting of CIISB (Czech Infrastructure for Integrative Structural Biology). 2023. ISSN 1211-5894.

BOUCHAL, Tomáš, Ivo DURNÍK a Petr KULHÁNEK. Bending of Canonical and G/T Mismatched DNAs. Journal of Chemical Information and Modeling. American Chemical Society, 2021, roč. 61, č. 12, s. 6000-6011. ISSN 1549-9596. Dostupné z: https://dx.doi.org/10.1021/acs.jcim.1c00731.

BOUCHAL, Tomáš, Ivo DURNÍK a Petr KULHÁNEK. Bending of Canonical and G/T Mismatched DNAs. In XXVI. Annual Congress of Czech and Slovak Societies for Biochemistry and Molecular Biology with cooperation of Austrian and German Biochemical Section, 2021. 2021. ISBN 978-80-907779-1-0.

TOMEČEK, Josef, Andrea ČABLOVÁ, Aneta HROMÁDKOVÁ, Jan NOVOTNÝ, Radek MAREK, Ivo DURNÍK, Petr KULHÁNEK, Zdeňka PRUCKOVÁ, Michal ROUCHAL, Lenka DASTYCHOVÁ a Robert VÍCHA. Modes of Micromolar Host-Guest Binding of beta-Cyclodextrin Complexes Revealed by NMR Spectroscopy in Salt Water. The Journal of Organic Chemistry. American Chemical Society, 2021, roč. 86, č. 6, s. 4483-4496. ISSN 0022-3263. Dostupné z: https://dx.doi.org/10.1021/acs.joc.0c02917.

KULKARNI, Shantanu Ganesh, Kristýna JELÍNKOVÁ, Marek NEČAS, Zdeňka PRUCKOVÁ, Michal ROUCHAL, Lenka DASTYCHOVÁ, Petr KULHÁNEK a Robert VÍCHA. A Photochemical/Thermal Switch Based on 4,4'-Bis(benzimidazolio)stilbene: Synthesis and Supramolecular Properties. ChemPhysChem. Weinheim: Wiley, 2020, roč. 21, č. 18, s. 2084-2095. ISSN 1439-4235. Dostupné z: https://dx.doi.org/10.1002/cphc.202000472.

BRADY, Kimberly G., Laura GILBERG, David SIGWALT, Joshua BISTANY-RIEBMAN, Steven MURKLI, Jared KLEMM, Petr KULHÁNEK, Vladimír ŠINDELÁŘ a Lyle ISAACS. Conformationally mobile acyclic cucurbit[n]uril-type receptors derived from an S-shaped methylene bridged glycoluril pentamer. Supramolecular Chemistry. Abingdon: Taylor & Francis Ltd., 2020, roč. 32, č. 9, s. 479-494. ISSN 1061-0278. Dostupné z: https://dx.doi.org/10.1080/10610278.2020.1795173.

BOUCHAL, Tomáš, Ivo DURNÍK, Viktor ILLÍK, Kamila RÉBLOVÁ a Petr KULHÁNEK. Importance of base-pair opening for mismatch recognition. Nucleic Acids Research. Oxford University Press, 2020, roč. 48, č. 20, s. 11322-11334. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkaa896.

RŮŽIČKA, Michal, Přemysl SOUČEK, Petr KULHÁNEK, Lenka RADOVÁ, L. FAJKUSOVA a Kamila RÉBLOVÁ. Bending of DNA duplexes with mutation motifs. DNA RESEARCH. OXFORD: OXFORD UNIV PRESS, 2019, roč. 26, č. 4, s. 341-352. ISSN 1340-2838. Dostupné z: https://dx.doi.org/10.1093/dnares/dsz013.

BOUCHAL, Tomáš, Ivo DURNÍK a Petr KULHÁNEK. Importance of Base-pair Probing for Mismatch Recognition. In Advances in Noncanonical Nucleic Acids, Rogaška Slatina, Slovenia. 2019. ISBN 978-961-6104-47-0.

ŠTĚPÁN, Jakub, Ivo KABELKA, Jaroslav KOČA a Petr KULHÁNEK. Behavior of BsoBI endonuclease in the presence and absence of DNA. Journal of Molecular Modeling. New York: Springer, 2018, roč. 24, č. 1, s. 22-31. ISSN 1610-2940. Dostupné z: https://dx.doi.org/10.1007/s00894-017-3557-8.

BOUCHAL, Tomáš, Ivo DURNÍK a Petr KULHÁNEK. Flexibility of DNA mismatches. In XIX. Setkání biochemiků a molekulárních biologů, Brno. 2018. 2018. ISBN 978-80-210-9069-9.

BOUCHAL, Tomáš, Ivo DURNÍK a Petr KULHÁNEK. Flexibility of DNA mismatches. In 2nd Users Conference of IT4Innovations, Ostrava, 2018. 2018.

DURNÍK, Ivo, Petr KULHÁNEK a Radek MAREK. Prediction of Binding of Ruthenium Anticancer Drugs into Macromolecular Drug Carriers. In 2nd Users Conference of IT4Innovations, Ostrava. 2018.

DURNÍK, Ivo, Petr KULHÁNEK a Radek MAREK. Ruthenium Anticancer Drugs and Macromolecular Drug Carriers: Prediction of Binding. In XIX. Setkání biochemiků a molekulárních biologů, Brno. 2018. ISBN 978-80-210-9069-9.

FIALA, Tomáš, Lucie LUDVÍKOVÁ, Dominik HEGER, Jan ŠVEC, Tomáš SLANINA, Ľubica VETRÁKOVÁ, Michal BABIAK, Marek NEČAS, Petr KULHÁNEK, Petr KLÁN a Vladimír ŠINDELÁŘ. Bambusuril as a One-Electron Donor for Photoinduced Electron Transfer to Methyl Viologen in Mixed Crystals. Journal of the American Chemical Society. WASHINGTON: American Chemical Society, 2017, roč. 139, č. 7, s. 2597-2603. ISSN 0002-7863. Dostupné z: https://dx.doi.org/10.1021/jacs.6b08589.

RŮŽIČKA, Michal, Petr KULHÁNEK, Lenka RADOVÁ, Andrea ČECHOVÁ, Naděžda ŠPAČKOVÁ, Lenka FAJKUSOVÁ a Kamila RÉBLOVÁ. DNA mutation motifs in the genes associated with inherited diseases. Plos one. San Francisco: Public Library of Science, 2017, roč. 12, č. 8, s. nestránkováno, 16 s. ISSN 1932-6203. Dostupné z: https://dx.doi.org/10.1371/journal.pone.0182377.

BOUCHAL, Tomáš, Ivo DURNÍK, Viktor ILLÍK a Petr KULHÁNEK. Influence of non-Watson-Crick base pairing on structure of DNA. In Modeling Interactions in Biomolecules VIII, Plzeň, Czech Republic, 3-8 September 2017. 2017.

RŮŽIČKA, Michal, Kamila RÉBLOVÁ a Petr KULHÁNEK. Study of structural and elastic properties of DNA mutation motifs using computational methods. In Modeling Interactions in Biomolecules VIII, Plzeň. 2017.

USTRNUL, Lukáš, Michal BABIAK, Petr KULHÁNEK a Vladimír ŠINDELÁŘ. A Cucurbituril Derivative That Exhibits Cation-Modulated Self Assembly. Journal of Organic Chemistry. WASHINGTON: AMER CHEMICAL SOC, 2016, roč. 81, č. 14, s. 6075-6080. ISSN 0022-3263. Dostupné z: https://dx.doi.org/10.1021/acs.joc.6b01288.

RÉBLOVÁ, Kamila, Lenka RADOVÁ, Andrea ČECHOVÁ, Michal RŮŽIČKA, Naděžda ŠPAČKOVÁ, Petr KULHÁNEK a Lenka FAJKUSOVÁ. Analysis of intrinsic properties of mutation motifs (coldspots-hotspots) in genes associated with inherited disorders using molecular dynamics methods. In 21st EuroQSAR. 2016.

BRANNÁ, Petra, Jarmila ČERNOCHOVÁ, Michal ROUCHAL, Petr KULHÁNEK, Martin BABINSKÝ, Radek MAREK, Marek NEČAS, Ivo KUŘITKA a Robert VÍCHA. Cooperative binding of cucurbit[n]urils and beta-cyclodextrin to heteroditopic imidazolium-based guests. The Journal of Organic Chemistry. Washington: American Chemical Society, 2016, roč. 81, č. 20, s. 9595-9604. ISSN 0022-3263. Dostupné z: https://dx.doi.org/10.1021/acs.joc.6b01564.

KUMARI, Manju, Stanislav KOZMON, Petr KULHÁNEK, Jakub ŠTĚPÁN, Igor TVAROŠKA a Jaroslav KOČA. Reaction Mechanism of O-GlcNAc Transferase Explored By QM/MM Molecular Dynamics. 2016.

MIKULÁŠEK, Kamil, Kamil JAROŇ, Petr KULHÁNEK, Miroslava BITTOVÁ a Jan HAVLIŠ. Sequence-dependent separation of trinucleotides by ion-interaction reversed-phase liquid chromatography A structure-retention study assisted by soft-modelling and molecular dynamics. Journal of Chromatography A. Amsterdam: Elsevier Science BV, 2016, roč. 1469, October, s. 88-95. ISSN 0021-9673. Dostupné z: https://dx.doi.org/10.1016/j.chroma.2016.09.060.

STŘELCOVÁ, Zora, Petr KULHÁNEK, Martin FRIÁK, Helge-Otto FABRITIUS, Michal PETROV, Joerg NEUGEBAUER a Jaroslav KOČA. The structure and dynamics of chitin nanofibrils in an aqueous environment revealed by molecular dynamics simulations. RSC Advances. Cambridge: Royal Society of Chemistry, 2016, roč. 6, č. 36, s. 30710-30721. ISSN 2046-2069. Dostupné z: https://dx.doi.org/10.1039/c6ra00107f.

ŠKULTÉTY, Michal a Petr KULHÁNEK. Computational study of carbonic anhydrase IX. In Modeling Interactions in Biomolecules VII, Praha, Czech Republic, 14-18 September, 2015, 2015. 2015.

BOUCHAL, Tomáš a Petr KULHÁNEK. Computational study of lectin PA-IIL. In Modeling Interactions in Biomolecules VII, Praha, Czech Republic, 14-18 September, 2015. 2015.

RÉBLOVÁ, Kamila, Petr KULHÁNEK a Lenka FAJKUSOVÁ. Computational study of missense mutations in phenylalanine hydroxylase. Journal of Molecular Modeling. New York: SPRINGER, 2015, roč. 21, č. 4, s. "nestránkováno", 10 s. ISSN 1610-2940. Dostupné z: https://dx.doi.org/10.1007/s00894-015-2620-6.

KUMARI, Manju, Stanislav KOZMON, Petr KULHÁNEK, Jakub ŠTĚPÁN, Igor TVAROŠKA a Jaroslav KOČA. Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study. Journal of Physical Chemistry B. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 119, č. 12, s. 4371-4381. ISSN 1520-6106. Dostupné z: https://dx.doi.org/10.1021/jp511235f.

USTRNUL, Lukáš, Petr KULHÁNEK, Tomáš LÍZAL a Vladimír ŠINDELÁŘ. Pressocucurbit[5]uril. Organic Letters. WASHINGTON, DC (USA): American Chemical Society, 2015, roč. 17, č. 4, s. 1022-1025. ISSN 1523-7060. Dostupné z: https://dx.doi.org/10.1021/acs.orglett.5b00123.

USTRNUL, Lukáš, Vladimír ŠINDELÁŘ a Petr KULHÁNEK. Pressocucurbit[5]uril: synthesis and supramolecular properties. In 10th International Symposium on Macrocyclic and Supramolecular Chemistry, ISMSC-2015, Strasbourg, France, June 28th-July 2nd, 2015. 2015.

USTRNUL, Lukáš, Vladimír ŠINDELÁŘ a Petr KULHÁNEK. Pressocucurbit[5]urils: Supramolecular properties. In 50th Advances in Organic, Bioorganic and Pharmaceutical Chemistry, "Liblice 2015", Olomouc, Czech republic, 6.-8.11.2015,. 2015.

ŠKULTÉTY, Michal a Petr KULHÁNEK. Theoretical study of carbonic anhydrase IX. In XIII Discussions in Structural Molecular Biology. 2015. ISSN 1211-5894.

NOVOTNÝ, Jan, Yevgen YURENKO, Petr KULHÁNEK a Radek MAREK. Tailoring the Properties of Quadruplex Nucleobases for Biological and Nanomaterial Applications. Physical Chemistry Chemical Physics. Cambridge: Royal Society of Chemistry, 2014, roč. 16, č. 29, s. 15241-15248. ISSN 1463-9076. Dostupné z: https://dx.doi.org/10.1039/C4CP00541D.

ŠTĚPÁN, Jakub, Petr KULHÁNEK, Milan LENČO, Zora STŘELCOVÁ, Aleš KŘENEK a Jaroslav KOČA. Nemesis - a molecular modeling package. Online. In Uli Fechner. Journal of Cheminformatics 2013, 5(Suppl 1). Goslar (GER): Chemistry Central, 2013, s. 13-14. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/1758-2946-5-S1-P12.

STANDARA, Stanislav, Petr KULHÁNEK, Radek MAREK a Michal STRAKA. 129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent. Journal of Computational Chemistry. New York: John Wiley & Sons, 2013, roč. 34, č. 22, s. 1890-1898. ISSN 0192-8651. Dostupné z: https://dx.doi.org/10.1002/jcc.23334.

NOVOTNÝ, Jan, Petr KULHÁNEK a Radek MAREK. Biocompatible Xanthine-Quadruplex Scaffold for Ion-Transporting DNA Channels. The Journal of Physical Chemistry Letters. Washington: American Chemical Society, 2012, roč. 3, č. 13, s. 1788-1792. ISSN 1948-7185. Dostupné z: https://dx.doi.org/10.1021/jz300559w.

CERNOCHOVA, Jarmila, Petra BRANNA, Michal ROUCHAL, Petr KULHÁNEK, Ivo KURITKA a Robert VICHA. Determination of Intrinsic Binding Modes by Mass Spectrometry: Gas-Phase Behavior of Adamantylated Bisimidazolium Guests Complexed to Cucurbiturils. Chemistry - A European Journal. Weinheim: WILEY-VCH Verlag, 2012, roč. 18, č. 43, s. 13633-13637. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.201201444.

SOLIMAN, Namat Ali, Petr KULHÁNEK a Jaroslav KOČA. Influence of stereochemistry on proton transfer in protonated tripeptide models. Journal of Molecular Modeling. New York: Springer, 2012, roč. 18, č. 3, s. 871-879. ISSN 1610-2940. Dostupné z: https://dx.doi.org/10.1007/s00894-011-1116-2.

MLÁDEK, Arnošt, Judit ŠPONEROVÁ, Petr KULHÁNEK, Xiang-Jun LU, Wilma K. OLSON a Jiří ŠPONER. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. Journal of Chemical Theory and Computation. Washington: ACS, 2012, roč. 8, č. 1, s. 335-347. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct200712b.

STŘELCOVÁ, Zora, Jakub ŠTĚPÁN, Petr KULHÁNEK, Paolo CARLONI a Jaroslav KOČA. Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism. In IX Discussions in Structural Molecular Biology, Nové Hrady. 2011.

MISHRA, Sushil Kumar, Jan ALÁN, Petr KULHÁNEK a Jaroslav KOČA. How to calculate binding energy in Protein-Carbohydrate complexes. In 5th THEORETICAL BIOPHYSICS INTERNATIONAL SYMPOSIUM, Madeira (Portugal), 8 - 12 June 2011. 2011.

BABINSKÝ, Martin, Petr KULHÁNEK, Viktor KOLMAN, Vladimír ŠINDELÁŘ a Radek MAREK. NMR and Computational Study of Supramolecular Interactions. In 26th Central European NMR Meeting Valtice. 2011.

KULHÁNEK, Petr, Letif MONES, Zora STŘELCOVÁ, Istvan SIMON, Monika FUXREITER a Jaroslav KOČA. PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS. In 8th Discussions in Structural Molecular Biology, Nové Hrady, Czech Republic. 2011.

KULHÁNEK, Petr, Letif MONES, Zora STŘELCOVÁ, Istvan SIMON, Monika FUXREITER a Jaroslav KOČA. PMFLib – A TOOLKIT FOR FREE ENERGY CALCULATIONS II. In Modeling Interactions in Biomolecules V, Kutná Hora, Czech Republic. 2011.

ŠTĚPÁN, Jakub, Zora STŘELCOVÁ, Petr KULHÁNEK a Jaroslav KOČA. Reaction Mechanism of MutH Enzyme - Quantum Mechanics/Molecular Mechanics Study 2. In XV. Setkání biochemiků a molekulárních biologů. 2011. ISBN 978-80-210-5594-0.

KOLMAN, Viktor, Martin BABINSKÝ, Petr KULHÁNEK, Radek MAREK a Vladimír ŠINDELÁŘ. Redistribution of electron density in pyridinium and pyrazinium guests induced by complexation with cucurbit[6]uril. New Journal of Chemistry. Oxford: Royal Society of Chemistry, 2011, roč. 35, č. 12, s. 2854-2859. ISSN 1144-0546. Dostupné z: https://dx.doi.org/10.1039/c1nj20631a.

STANDARA, Stanislav, Petr KULHÁNEK, Radek MAREK, Jan HORNÍČEK, Petr BOUŘ a Michal STRAKA. Simulation of 129Xe NMR chemical shift of Xe@C60 dissolved in liquid benzene. In DFT 2011 Athens : 14th International Density Functional Theory Conference (DFT). 2011.

STANDARA, Stanislav, Petr KULHÁNEK, Radek MAREK, Jan HORNÍČEK, Petr BOUŘ a Michal STRAKA. Simulations of 129 Xe NMR chemical shift of atomic xenon dissolved in liquid benzene. Theoretical Chemistry Accounts. SPRINGER, 2011, roč. 129, 3-5, s. 677-684. ISSN 1432-881X. Dostupné z: https://dx.doi.org/10.1007/s00214-011-0930-z.

ALÁN, Jan, Eva DEJMKOVÁ, Petr KULHÁNEK, Jaroslav KOČA a Michaela WIMMEROVÁ. Thermodynamics behind CV-IIL binding of saccharides. In 16th European Carbohydrates Symposium. 2011. ISBN 978-88-900948-8-0.

KULHÁNEK, Petr, Jan ALÁN a Jaroslav KOČA. Virtual screening and in silico design of novel inhibitors of bacterial lectins. In Modeling Interactions in Biomolecules V, Kutná Hora, Czech Republic. 2011.

ALÁN, Jan, Petr KULHÁNEK a Jaroslav KOČA. Virtual screening and in sillico design of novel inhibitors of bacterial lectins. In XV. Setkání biochemiků a molekulárních biologů. 2011. ISBN 978-80-210-5549-0.

RÉBLOVÁ, Kamila, Zora STŘELCOVÁ, Petr KULHÁNEK, Ivana BEŠŠEOVÁ, David H. MATHEWS, Keith VAN NOSTRAND, Ilyas YILDIRIM, Douglas H. TURNER a Jiří ŠPONER. An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5 '-UAA/5 '-GAN Internal Loops Studied by Molecular Dynamics Methods. Journal of Chemical Theory and Computation. 2010, roč. 2010, č. 6, s. 910-929, 19 s. ISSN 1549-9618.

KMUNÍČEK, Jan, Zora STŘELCOVÁ a Petr KULHÁNEK. Applicability of Free Energy Calculations using High-Throughput Grid Approach. In Proceedings of International Symposium on Grid Computing (ISGC) 2010. 2010.

KMUNÍČEK, Jan, Daniel KOUŘIL, Luděk MATYSKA, Zora STŘELCOVÁ, Petr KULHÁNEK, Jaroslav KOČA a Eric YEN. Catch-All Virtual Organizations - Solution for Heterogeneous and Disperse Grid Users Communities. In Lin, S. C.; Yen, E. Managed Grids and Cloud Systems in the Asia-Pacific Research Community. New York: Springer, 2010, s. 299-309. ISBN 978-1-4419-6468-7. Dostupné z: https://dx.doi.org/10.1007/978-1-4419-6469-4_22.

ALÁN, Jan, Petr KULHÁNEK a Jaroslav KOČA. Computational study of lectin-carbohydrate interactions. In XIV. Setkání biochemiků a molekulárních biologů. 2010. ISBN 978-80-210-5164-5.

STŘELCOVÁ, Zora, Petr KULHÁNEK a Jaroslav KOČA. Computational Study of the MutH Enzyme Reactivity. In XIV. Setkání biochemiků a molekulárních biologů. 2010.

KULHÁNEK, Petr. Distributed Way of Biomolecular Conformational Space Exploration - Experience of grid - CICADA Tool Utilization. 2010.

ALÁN, Jan, Petr KULHÁNEK a Jaroslav KOČA. Employment of free energy calculations to estimation of carbohydrates affinities towards PA-IIL superfamily lectins. In Materials Structure in Chemistry, Biology, Physics and Technology. 2010. ISSN 1211-5894.

ŠTĚPÁN, Jakub, Petr KULHÁNEK, Zdeněk KŘÍŽ, Jan KMUNÍČEK, Jaroslav KOČA a Luděk MATYSKA. grid-CICADA: Efficient Explorer of Conformational Space of Biomolecular Systems. In 5th EGEE User Forum. 2010.

KOLMAN, Viktor, Petr KULHÁNEK a Vladimír ŠINDELÁŘ. Inclusion of Carboxyl Function Inside of Cucurbiturils and its Use in Molecular Switches. Chemistry – An Asian Journal. WILEY-VCH, 2010, roč. 5, č. 11, s. 6926-6931, 7 s. ISSN 1861-4728.

BABINSKÝ, Martin, Petr KULHÁNEK, Viktor KOLMAN, Vladimír ŠINDELÁŘ a Radek MAREK. NMR and Computational Study of Supramolecular Complexes. In 1st EAST-NMR Young Investigators Meeting. 2010.

STŘELCOVÁ, Zora, Petr KULHÁNEK a Jaroslav KOČA. Reaction Mechanism of MutH Enzyme: Quantum Mechanics/Molecular Mechanics Study. In Materials Structure in Chemistry, Biology, Physics and Technology. 2010. ISSN 1211-5894.

STANDARA, Stanislav, Petr KULHÁNEK, Petr BOUŘ a Michal STRAKA. Simulation of 129Xe NMR shift of Xe dissolved in benzene. In Joint EUROMAR 2010 and 17th ISMAR Conference - A World Wide Magnetic Resonance Conference. 2010.

STANDARA, Stanislav, Petr KULHÁNEK, Radek MAREK, Jan HORNÍČEK, Petr BOUŘ a Michal STRAKA. Simulations of 129Xe chemical shift of atomic xenon dissolved in liquid benzene. In Winter School in Theoretical Chemistry 2010 - Accurate Molecular Structure by Experiment and Theory. 2010.

FUKAL, Jiří, Petr KULHÁNEK, Eva FADRNÁ a Jaroslav KOČA. Study of HincII endonuclease by molecular dynamics methods. In 8th Discussions in Structural Molecular Biology. 2010.

BABINSKÝ, Martin, Petr KULHÁNEK, Viktor KOLMAN, Vladimír ŠINDELÁŘ a Radek MAREK. Štúdium supramolekulárnych komplexov cucurbit[6]urilu pomocou NMR spektroskopie a výpočtovej chémie. In Pokroky v organické, bioorganické a farmaceutické chemii – „LIBLICE 2010“. 2010. ISSN 1213-7103.

KULHÁNEK, Petr, Letif MONES, Istvan SIMON a Monika FUXREITER. Computational Study of MutH Recognition and Catalysis. In Modelling Interactions in Biomolecules IV. 2009. ISBN 978-80-7378-098-2.

KOLMAN, Viktor, Radek MAREK, Zora STŘELCOVÁ, Petr KULHÁNEK, Marek NEČAS, Jan ŠVEC a Vladimír ŠINDELÁŘ. Electron Density Shift in Imidazolium Derivatives upon Complexation with Cucurbit[6]uril. Chemistry - A European Journal. WILEY-VCH, 2009, roč. 15, č. 28, s. 6926-6931. ISSN 0947-6539. Dostupné z: https://dx.doi.org/10.1002/chem.200900570.

SOLT, Ivan, Petr KULHÁNEK, Istvan SIMON, Steven WINFIELD, Mike C PAYNE, Gabor CSANYI a Monika FUXREITER. Evaluating Boundary Dependent Errors in QM/MM Simulations. Journal of Physical Chemistry B. New York: American Chemical Society, 2009, roč. 2009, 113(17), s. 5728-5735, 7 s. ISSN 1520-6106.

KOLMAN, Viktor, Radek MAREK, Zora STŘELCOVÁ, Petr KULHÁNEK, Marek NEČAS, Jan ŠVEC a Vladimír ŠINDELÁŘ. Charge Localization on Imidazolium Ring upon Complexation with Cucurbit[6]uril. In First International Conference on Cucurbiturils. 2009.

KOLMAN, Viktor, Radek MAREK, Zora STŘELCOVÁ, Petr KULHÁNEK, Marek NEČAS, Jan ŠVEC a Vladimír ŠINDELÁŘ. Charge Localization on Imidazolium Ring upon Complexation with Cucurbit[6]uril. In 10th International Conference on Calixarenes. 2009.

STŘELCOVÁ, Zora, Petr KULHÁNEK, Jan KMUNÍČEK, Jaroslav KOČA a Luděk MATYSKA. Implementation and Testing of Multiple Walkers Approach Based Free Energy Calculations in the Grid Environment. In GCCP Proceedings. Bratislava, Slovakia: Institute of Informatics SAS, 2009, s. 29-36, 7 s. ISBN 978-80-970145-1-3.

ŠTĚPÁN, Jakub, Petr KULHÁNEK, Jaroslav KOČA a Navnit Kumar MISHRA. Implementation of Parallel Analyzes of Molecular Dynamics Simulation Trajectories. 2009.

STŘELCOVÁ, Zora, Petr KULHÁNEK, Jan KMUNÍČEK, Jaroslav KOČA a Luděk MATYSKA. Large-Scale Free Energy Calculations as Showcase of Worldwide Grid Usability. In 4th EGEE User Forum/OGF 25 and OGF Europe's 2nd International Event. 2009.

KLVAŇA, Martin, Martina PAVLOVÁ, Táňa KOUDELÁKOVÁ, Radka CHALOUPKOVÁ, Pavel DVOŘÁK, Zbyněk PROKOP, A. STSIAPANAVA, Michal KUTÝ, Ivana KUTÁ-SMATANOVÁ, J. DOHNÁLEK, Petr KULHÁNEK, R. WADE a Jiří DAMBORSKÝ. Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. JOURNAL OF MOLECULAR BIOLOGY. 2009, roč. 2009, č. 00, s. 0000-0000, 10 s. ISSN 0022-2836.

MONES, Letif, Petr KULHÁNEK, Istvan SIMON, Alessandro LAIO a Monika FUXREITER. The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions. Journal of Physical Chemistry B. New York: American Chemical Society, 2009, roč. 2009, 113(22), s. 7867-7873, 6 s. ISSN 1520-6106.

MATOUŠEK, Jiří, Michal ČAJAN, Petr KULHÁNEK a Jaroslav KOČA. Mechanism of Hydrogen Bond Array Isomerization in Tetrahydroxycalix[4]arene and Tetrahydroxythiacalix[4]arene. Journal of Physical Chemistry A. USA: The American Chemical Society, 2008, roč. 112, č. 1, s. 1076-1084. ISSN 1089-5639.

MISHRA, Navnit Kumar, Petr KULHÁNEK, Lenka ŠNAJDROVÁ, Martin PETŘEK, Anne IMBERTY a Jaroslav KOČA. Molecular dynamics study of Pseudomonas eruginosa lectin-II complexed with monosaccharides. Proteins: Structure, Function, and Bioinformatics. Wiley, 2008, roč. 72, č. 1, s. 382–392. ISSN 0887-3585.

KLVAŇA, Martin, Martina PAVLOVÁ, Táňa KOUDELÁKOVÁ, Radka CHALOUPKOVÁ, Radka CHALOUPKOVÁ, Alena STSIAPANAVA, Michal KUTÝ, Ivana KUTÁ-SMATANOVÁ, J. DOHNÁLEK, Petr KULHÁNEK, R.C. WADE a Jiří DAMBORSKÝ. Pathways and Mechanisms for Product Exit and Water Exchange in Engineered Haloalkane Dehalogenase DhaA Exploredusing Classical and Random Acceleration Molecular Dynamics Simulations. 2008.

MISHRA, Navnit Kumar, Petr KULHÁNEK, Zdenek KRIZ, Michaela WIMMEROVA a Jaroslav KOCA. Computational Studies on PA-IIL Lectin-Carbohydrate Interactions. In Materials Structure in Chemistry, Biology, Physics and Technology. 2007. ISSN 1211-5894.

RÉBLOVÁ, Kamila, Eva FADRNÁ, Sarzynska JOANNA, Tadeusz KULINSKI, Petr KULHÁNEK, Eric ENNIFAR, Jaroslav KOČA a Jiri SPONER. Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by Molecular Dynamics. Biophysical Journal. New York, USA: Rockefeller University, 2007, roč. 93, č. 11, s. 3932-3949. ISSN 0006-3495.

MONES, Letif, Petr KULHÁNEK, Jan FLORIAN, Istvan SIMON a Monika FUXREITER. Probing the two-metal ion mechanism in the restriction endonuclease BamHI. Biochemistry. 2007, roč. 2007, 46(50), s. 14514-14523, 9 s. ISSN 0006-2960.

PETŘEK, Martin, Jan KMUNÍČEK a Petr KULHÁNEK. Computational Chemistry Achievements within VOCE Environment. Geneva, Switzerland, 2006.

MATOUŠEK, Jiří, Petr KULHÁNEK, Michal ČAJAN a Jaroslav KOČA. Effect of Solvation on Pinched Cone-Pinched Cone Interconversion of Tetraethoxycalix[4]arene and Tetraethoxythiacalix[4]arene. Journal of Physical Chemistry A. 2006, roč. 110, č. 3, s. 861-867. ISSN 1089-5639.

KMUNÍČEK, Jan, Martin PETŘEK a Petr KULHÁNEK. Charon Extension Layer - Universal Toolkit for Grid Applications and Computational Jobs Maintenance. Krakow, Poland: CRW06, 2006.

KLVAŇA, Martin, R.C. WADE, Petr KULHÁNEK a Jiří DAMBORSKÝ. Modelling of Product Release and Identification of Export Routes in Haloalkane Dehalogenase DhaA. 2006.

SOLIMAN, Namat Ali, Petr KULHÁNEK a Jaroslav KOČA. Stereochemistry influence on proton transfer in protonated tripeptide model. JOURNAL OF PEPTIDE SCIENCE. ENGLAND: JOHN WILEY & SONS LTD, 2006, roč. 12, č. 2, s. 191-191. ISSN 1075-2617.

KULHÁNEK, Petr, Martin PETŘEK a Jan KMUNÍČEK. CHARON System - A Framework for Comfortable Grid Applications & Jobs Management. Pisa, 2005.

KMUNÍČEK, Jan, Petr KULHÁNEK a Martin PETŘEK. CHARON System - Framework for Applications and Jobs Management in Grid Environment. In Cracow Grid Workshop 05. Cracow: Academic Computer Center CYFRONET AGH, Cracow, Poland, 2005, s. 332-340. ISBN 83-915141-5-3.

ŠPONER, Judit E, Naděžda ŠPAČKOVÁ, Petr KULHÁNEK, Jerzy LESZCZYNSKI a Jiří ŠPONER. Non-Watson-Crick base pairing in RNA. Quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family. JOURNAL OF PHYSICAL CHEMISTRY A. 2005, roč. 109, č. 10, s. 2292-2301. ISSN 1089-5639.

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY a Jaroslav KOČA. Molecular dynamics simulations of glycosyltransferase LgtC. Carbohydrate Research. 2004, roč. 339, č. 5, s. 995-1006. ISSN 0008-6215.

KULHÁNEK, Petr, Milan POTÁČEK a Jaroslav KOČA. Quantum-chemical insight into mechanism of combined intra-intermolecular cycloaddition. Collection of Czechoslovak Chemical Communications. Prague, 2004, roč. 69/2004, č. 1, s. 231-241. ISSN 0010-0765.

KULHÁNEK, Petr, Edward W. SCHLAG a Jaroslav KOČA. A Novel Mechanism of Proton Transfer in Protonated Peptides. Journal of the American Chemical Society. Washington, DC., USA: American Chemical Society, 2003, roč. 125, č. 45, s. 13678-13679, 1 s. ISSN 0002-7863.

KULHÁNEK, Petr, Robert VÍCHA, Tomáš POSPÍŠIL, Richard ČMELÍK a Milan POTÁČEK. Automatizovaný systém zkoušení KERBEROS v2.0. Chemické listy. Praha: Česká společnost chemická, 2003, roč. 97, č. 8, s. 703-704. ISSN 0009-2770.

KULHÁNEK, Petr, Edward W. SCHLAG a Jaroslav KOČA. Mechanism of Proton Transfer in Short Protonated Oligopeptides. 1. N-Methylacetamide and N2-Acetyl-N1-methylglycinamide. J. Phys. Chem. A. American Chemical Society, 2003, roč. 107, č. 30, s. 5789-5797, 8 s. ISSN 1089-5639.

LITERÁK, Jaromír, Stanislav RELICH, Petr KULHÁNEK a Petr KLÁN. Temperature Dependent Photochemical Cleavage of 2,5-Dimethylphenacyl Esters. Molecular Diversity. Basel, Switzerland: Kluwer, 2003, roč. 7, 2-4, s. 265-271. ISSN 1381-1991.

KULHÁNEK, Petr a Jaroslav KOČA. Influence of Water Molecule To Proton Transfer in Dipeptide Model. In International Chemometric Conference, CHEMOMETRICS VI. 1. vyd. Brno: Masaryk University, 2002, s. O20, 1 s. ISBN 80-210-2918-8.

MAN, Stanislav, Petr KULHÁNEK a Milan POTÁČEK. Kombinované intra-intermolekulární criss-cross cykloadice allenylazinů. Chem. listy. Praha: Česká společnost chemická, 2002, roč. 96, č. 6, s. 404. ISSN 0009-2770.

KULHÁNEK, Petr a Jaroslav KOČA. Kvantově-chemická studie přenosu protonu v oligopeptidech. Chem. listy. Praha: Česká společnost chemická, 2002, roč. 96, č. 6, s. 425. ISSN 0009-2770.

MAN, Stanislav, Petr KULHÁNEK, Milan POTÁČEK a Marek NEČAS. New fused heterocycles by combined intra-intermolecular criss-cross cycloaddition of nonsymmetrical azines. Tetrahedron Letters. Oxford: Pergamon - Elsevier Science, 2002, roč. 36, č. 43, s. 6431-6433. ISSN 0040-4039.

MAN, Stanislav, Petr KULHÁNEK, Hana ZACHOVÁ a Milan POTÁČEK. New Type of ortho-peri-fused Heterocycles via Combined Intra-intermolecular Cycloaddition. In 9th Blue Danube Symposium on Heterocyclic Chemistry, Book of Abstracts. 1. vyd. Bratislava, Slovak Republic: Publishing House of Slovak University of Technology, Bratislava, 2002, s. 180. ISBN 80-227-1705-3.

KLÁN, Petr, Radovan RŮŽIČKA, Dominik HEGER, Jaromír LITERÁK, Petr KULHÁNEK a André LOUPY. Temperature-sensitive photochemical aromatic substitution on 4-nitroanisole. Photochemical and Photobiological Sciences. Cambridge, United Kingdom: Royal Society of Chemistry, 2002, roč. 1, č. 12, s. 1012-1017. ISSN 1474-905X.

KULHÁNEK, Petr, Robert VÍCHA, Richard ČMELÍK a Milan POTAČEK. Automatizovaný systém zkoušení KERBEROS. In Sborník príspevkov 53. zjazd Chemických spoločností. 1. vyd. Banká Bystrica: FPV Univerzita Mateja Bela v Banskej Bystrici, 2001, s. 138. ISBN 80-89029-22-1.

KULHÁNEK, Petr, Stanislav MAN a Milan POTÁČEK. Nesymetrický allenylazin jako prekurzor pro smíšené intra-inter-molekulární criss-cross cykloadice. In Zborník príspevkov (53. Zjazd chemických spoločností). 1. vyd. Bánská Bystrica: FPV Univerzita Mateja Bela v Banskej Bystrici, 2001, s. 166-167. č. svazku 3. ISBN 80-89029-24-8.

POTÁČEK, Milan, Petr KULHÁNEK a Jiří VERNER. Criss-cross Cycloaddition - Source of New Heterocyclic Compounds. In Boook of Abstracts (17 th International Congress of Heterocyclic Chemistry). 1. vyd. Wien: Vienna University of Technology, 1999, s. 197. Book of Abstracts (17th ICHC).