Výpis publikací

KEOWN, Jeremy, Alaa BAAZAOUI, Marek ŠEBESTA, Richard ŠTEFL, Loic CARRIQUE, Ervin FODOR a Jonathan M GRIMES. Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II. Journal of Virology. WASHINGTON: American Society for Microbiology, 2024, roč. 98, č. 5, s. 1-15. ISSN 0022-538X. Dostupné z: https://dx.doi.org/10.1128/jvi.00138-24.

ZAPLETAL, David, Karel KUBÍČEK, Petr SVOBODA a Richard ŠTEFL. Dicer structure and function: conserved and evolving features. EMBO reports. Wiley, 2023, roč. 24, č. 7, s. 1-13. ISSN 1469-221X. Dostupné z: https://dx.doi.org/10.15252/embr.202357215.

HAŠANOVÁ, Zdenka, Veronika KLÁPŠŤOVÁ, Odil PORRUA, Richard ŠTEFL a Marek ŠEBESTA. Human senataxin is a bona fide R-loop resolving enzyme and transcription termination factor. Nucleic Acids Research. Oxford University Press, 2023, roč. 51, č. 6, s. 2818-2837. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkad092.

LONG, Qilin, Marek ŠEBESTA, Kateřina ŠEDOVÁ, Vojtěch HALUZA, Adele ALAGIA, Zhichao LIU, Richard ŠTEFL a Monika GULLEROVA. The phosphorylated trimeric SOSS1 complex and RNA polymerase II trigger liquid-liquid phase separation at double-strand breaks. Cell Reports. Elsevier, 2023, roč. 42, č. 12, s. 1-25. ISSN 2211-1247. Dostupné z: https://dx.doi.org/10.1016/j.celrep.2023.113489.

KASILIAUSKAITE, Aiste, Karel KUBÍČEK, Tomáš KLUMPLER, Martina ZÁNOVÁ, David ZAPLETAL, Eliska KOUTNA, Jiří NOVÁČEK a Richard ŠTEFL. Cooperation between intrinsically disordered and ordered regions of Spt6 regulates nucleosome and Pol II CTD binding, and nucleosome assembly. Nucleic acids research. Oxford: Oxford University Press, 2022, roč. 50, č. 10, s. 5961-5973. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkac451.

ZAPLETAL, David, Karel KUBÍČEK, Martina ZÁNOVÁ, Radek MALIK, Marek ŠEBESTA, Jiří NOVÁČEK, Petr SVOBODA a Richard ŠTEFL. Cryo-EM reveals the structural basis for the regulatory function of HEL1 domain in vertebrate DICERs. In Instruct Biennial Structural Biology ConferenceMuntgebouw, Utrecht, The Netherlands | 19-20 May, 2022. 2022.

ZAPLETAL, David, Eliska TABORSKA, Josef PASULKA, Radek MALIK, Karel KUBÍČEK, Martina ZÁNOVÁ, Christian MUCH, Marek ŠEBESTA, Valeria BUCCHERI, Filip HORVAT, Irena JENICKOVA, Michaela PROCHAZKOVA, Jan PROCHAZKA, Matyáš PINKAS, Jiří NOVÁČEK, Diego F JOSEPH, Radislav SEDLACEK, Carrie BERNECKY, Donal CARROLL, Richard ŠTEFL a Petr SVOBODA. Structural and functional basis of mammalian microRNA biogenesis by Dicer. Molecular Cell. CAMBRIDGE: CELL PRESS, 2022, roč. 82, č. 21, s. 4064-4079. ISSN 1097-2765. Dostupné z: https://dx.doi.org/10.1016/j.molcel.2022.10.010.

APPEL, Lisa-Marie, Vedran FRANKE, Melania BRUNO, Irina GRISHKOVSKAYA, Aiste KASILIAUSKAITE, Tanja KAUFMANN, Ursula E. SCHOEBERL, Martin G. PUCHINGER, Sebastian KOSTRHON, Carmen EBENWALDNER, Marek ŠEBESTA, Etienne BELTZUNG, Karl MECHTLER, Gen LIN, Anna VLASOVA, Martin LEEB, Rushad PAVRI, Alexander STARK, Altuna AKALIN, Richard ŠTEFL, Carrie BERNECKY, Kristina DJINOVIC-CARUGO a Dea SLADE. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. London: Nature Publishing Group, 2021, roč. 12, č. 1, s. 6078-6101. ISSN 2041-1723. Dostupné z: https://dx.doi.org/10.1038/s41467-021-26360-2.

KASILIAUSKAITE, Aiste, Richard ŠTEFL, Tomáš KLUMPLER a Jiří NOVÁČEK. A Structural Basis for the Cross-Talk Between Histones and RNA Polymerase II. In CEITEC PhD Conference. 2020.

LINHARTOVÁ, Kateřina, Jakub MACOŠEK, Veronika JANŠTOVÁ, Eliška ŠMIŘÁKOVÁ, Karel KUBÍČEK a Richard ŠTEFL. Recognition of RNA Polymerase II C-terminal domain by RPRD2. In CEITEC PhD Conference. 2020.

KLÁPŠŤOVÁ, Veronika, Marek ŠEBESTA, Jiří NOVÁČEK a Richard ŠTEFL. Structural Characterization of the Interaction Between BRCA1-BARD1 and RNA Polymerase II. In CEITEC PhD Conference. 2020.

HAN, Z., Olga JASNOVIDOVA, N. HAIDARA, A. TUDEK, Karel KUBÍČEK, D. LIBRI, Richard ŠTEFL a O. PORRUA. Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. EMBO Journal. Hoboken (USA): WILEY-BLACKWELL, 2020, roč. 39, č. 7, s. 101548-101569. ISSN 0261-4189. Dostupné z: https://dx.doi.org/10.15252/embj.2019101548.

BRÁZDA, Pavel, Magdaléna KREJČÍKOVÁ, Aiste KASILIAUSKAITE, Eliška ŠMIŘÁKOVÁ, Tomáš KLUMPLER, Robert VÁCHA, Karel KUBÍČEK a Richard ŠTEFL. Yeast Spt6 Reads Multiple Phosphorylation Patterns of RNA Polymerase II C-Terminal Domain In Vitro. Journal of Molecular Biology. Academic Press, 2020, roč. 432, č. 14, s. 4092-4107. ISSN 0022-2836. Dostupné z: https://dx.doi.org/10.1016/j.jmb.2020.05.007.

BRÁZDA, Pavel, Ondrej ŠEDO, Karel KUBÍČEK a Richard ŠTEFL. Efficient and robust preparation of tyrosine phosphorylated intrinsically disordered proteins. BioTechniques. UNITED HOUSE, 2 ALBERT PL, LONDON N3 1QB: FUTURE SCI LTD, 2019, roč. 67, č. 1, s. 16-22. ISSN 0736-6205. Dostupné z: https://dx.doi.org/10.2144/btn-2019-0033.

JASNOVIDOVA, Olga, Magdaléna KREJČÍKOVÁ, Karel KUBÍČEK a Richard ŠTEFL. Structural insight into recognition of phosphorylated threonine-4 of RNA polymerase II C-terminal domain by Rtt103p. EMBO reports. Hoboken: Wiley-Blackwell, 2017, roč. 18, č. 6, s. 906-913. ISSN 1469-221X. Dostupné z: https://dx.doi.org/10.15252/embr.201643723.

JASNOVIDOVA, Olga, Tomáš KLUMPLER, Karel KUBÍČEK, Sergei KALYNYCH, Pavel PLEVKA a Richard ŠTEFL. Structure and dynamics of the RNAPII CTDsome with Rtt103. Proceeding of the National Academy of Sciences of the USA. The Academy, 2017, roč. 114, č. 42, s. 11133-11138. ISSN 0027-8424. Dostupné z: https://dx.doi.org/10.1073/pnas.1712450114.

JASNOVIDOVA, Olga, Magdaléna KREJČÍKOVÁ, Karel KUBÍČEK a Richard ŠTEFL. Recognition of phosphorylated threonine-4 of RNA polymerase II C-terminal domain by 3 '-end processing apparatus. In 41st FEBS Congress on Molecular and Systems Biology for a Better Life. 2016. ISSN 1742-464X.

KUBÍČEK, Karel, Magdaléna KREJČÍKOVÁ, Pavel BRÁZDA, Eliška ŠMIŘÁKOVÁ, Jiří NOVÁČEK, Patrick CRAMER a Richard ŠTEFL. What are the key aspects of interaction between RNA polymerase II C-terminal domain phosphorylated on tyrosine-1 and the elongation factors. In 41st FEBS Congress on Molecular and Systems Biology for a Better Life. 2016. ISSN 1742-464X.

KŘENEK, Aleš, Karel KUBÍČEK, Richard ŠTEFL a Jiří FILIPOVIČ. Accurate Fitting SAXS Curves with NMR Structure Ensembles. Online. In Simon Lin, Vicky Huang. Proceedings of International Symposium on Grids and Clouds 2015. Pissa: Proceedings of Science, 2015, s. nestránkováno, 9 s. ISSN 1824-8039.

KLUMPLER, Tomáš, Tereza GERGURI, Olga JASNOVIDOVA, Lumír KREJČÍ, Karel KUBÍČEK, Daniel NĚMEČEK, Vojtěch SEDLÁČEK a Richard ŠTEFL. Biological Small Angle X-ray Scattering at CEITEC-MU. Materials Structure in Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2015, roč. 22, č. 3, s. 127-132. ISSN 1211-5894.

KREPL, Miroslav, Marek HAVRILA, Petr STADLBAUER, Pavel BANÁŠ, Michal OTYEPKA, Josef PASULKA, Richard ŠTEFL a Jiří ŠPONER. Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes? Journal of Chemical Theory and Computation. WASHINGTON: AMER CHEMICAL SOC, 2015, roč. 11, č. 3, s. 1220-1243. ISSN 1549-9618. Dostupné z: https://dx.doi.org/10.1021/ct5008108.

HROŠŠOVÁ, Dominika, Tomáš ŠIKORSKÝ, David POTĚŠIL, Marek BARTOŠOVIČ, Josef PASULKA, Zbyněk ZDRÁHAL, Richard ŠTEFL a Štěpánka VAŇÁČOVÁ. RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3 '-end extended forms of snRNAs. Nucleic Acids Research. Oxford: Oxford University Press, 2015, roč. 43, č. 8, s. 4236-4248. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gkv240.

TUDEK, Agnieszka, Odil Porrua FUERTE, Tomasz KABZINSKI, Michael LIDSCHREIBER, Karel KUBÍČEK, Andrea FOŘTOVÁ, Francoise LACROUTE, Štěpánka VAŇÁČOVÁ, Patrick CRAMER, Richard ŠTEFL a Domenico LIBRI. Molecular Basis for Coordinating Transcription Termination with Noncoding RNA Degradation. Molecular Cell. CAMBRIDGE: CELL PRESS, 2014, roč. 55, č. 3, s. 467-481. ISSN 1097-2765. Dostupné z: https://dx.doi.org/10.1016/j.molcel.2014.05.031.

BAČÍKOVÁ, Veronika, Josef PASULKA, Karel KUBÍČEK a Richard ŠTEFL. Structure and semi-sequence-specific RNA binding of Nrd1. Nucleic Acids Research. United Kingdom: Oxford University Press, 2014, roč. 42, č. 12, s. 8024-8038. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gku446.

JASNOVIDOVA, Olga a Richard ŠTEFL. The CTD code of RNA polymerase II: a structural view. Wiley Interdisciplinary Reviews: RNA. Hoboken, USA: WILEY-BLACKWELL, 2013, roč. 4, č. 1, s. 1-16. ISSN 1757-7004. Dostupné z: https://dx.doi.org/10.1002/wrna.1138.

HOLUB, Peter, Jana LALÁKOVÁ, Hana ČERNÁ, Josef PASULKA, Marie SÁRAZOVÁ, Kristýna HRAZDILOVÁ, Maria SAŇUDO ARCE, Fruzsina HÓBOR, Richard ŠTEFL a Štěpánka VAŇÁČOVÁ. Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation. Nucleic Acids Research. Oxford: Oxford University Press, 2012, roč. 40, č. 12, s. 5679-5693. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gks223.

PORRUA-FUERTE, Odil, Fruzsina HÓBOR, Jocelyne BOULAY, Karel KUBÍČEK, Yves D’AUBENTON-CARAFA, Rajani Kanth GUDIPATI, Richard ŠTEFL a Domenico LIBRI. In vivo SELEX reveals novel sequence and structural determinants of Nrd1-Nab3-Sen1 dependent transcription termination. EMBO Journal. NEW YORK: NATURE PUBLISHING GROUP, 2012, roč. 31, č. 19, s. 3935-3948. ISSN 0261-4189. Dostupné z: https://dx.doi.org/10.1038/emboj.2012.237.

ŠIKORSKÝ, Tomáš, Fruzsina HÓBOR, Eva KRIŽANOVÁ, Josef PASULKA, Karel KUBÍČEK a Richard ŠTEFL. Recognition of asymmetrically dimethylated arginine by TDRD3. Nucleic Acids Research. Oxford: Oxford University Press, 2012, roč. 40, č. 22, s. 11748-11755. ISSN 0305-1048. Dostupné z: https://dx.doi.org/10.1093/nar/gks929.

ŠTEFL, Richard a Vladimír SKLENÁŘ. RNA. In Ivano Pertini, Kathleen S. McGreevy, Giacomo Parigi. NMR of Biomolecules, Towards Mechanistic System Biology. 1. vyd. Weinheim, Německo: Wiley-Blackwell, 2012, s. 119-135. ISBN 978-3-527-32850-5.

KUBÍČEK, Karel, Hana ČERNÁ, Peter HOLUB, Josef PASULKA, Dominika HROŠŠOVÁ, Frank LOEHR, Ctirad HOFR, Štěpánka VAŇÁČOVÁ a Richard ŠTEFL. Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1. Genes & Development. New York: Cold Spring Harbor Laboratory Press, 2012, roč. 26, č. 17, s. 1891-1896. ISSN 0890-9369. Dostupné z: https://dx.doi.org/10.1101/gad.192781.112.

HÓBOR, Fruzsina, Roberto PERGOLI, Karel KUBÍČEK, Dominika HROŠŠOVÁ, Veronika BAČÍKOVÁ, Michal ZIMMERMANN, Josef PASULKA, Ctirad HOFR, Štěpánka VAŇÁČOVÁ a Richard ŠTEFL. Recognition of transcription termination signal by the nuclear polyadenylated RNA-binding (Nab)3 protein. The Journal of Biological Chemistry. Am. Soc. for Biochem. and Mol. Biol., 2011, roč. 286, č. 5, s. 3645-3657. ISSN 0021-9258. Dostupné z: https://dx.doi.org/10.1074/jbc.M110.158774.

KUBÍČEK, Karel, Josef PASULKA, Hana ČERNÁ, Frank LÖHR a Richard ŠTEFL. 1H, 13C, and 15N resonance assignments for the CTD-Interacting Domain of Nrd1 bound to Ser5-phosphorylated CTD of RNA Polymerase II. Biomolecular NMR Assignments. Netherlands: Springer Netherlands, 2011, roč. 5, č. 2, s. 203-205. ISSN 1874-2718. Dostupné z: https://dx.doi.org/10.1007/s12104-011-9300-y.

PASULKA, Josef, Jaroslav KOČA a Richard ŠTEFL. The computational view inside the dynamical behavior of the RNA-binding motive. In 8th Discussions in Structural Molecular Biology, Nove Hrady, March 18 - 20, 2010. 2010. ISSN 1211-5894.

ŠTEFL, Richard, Florian OBERSTRASS, Jeniffer HOOD, Muriel JOURDAN, Michal ZIMMERMANN, Lenka SKŘÍŠOVSKÁ, Christophe MARIS, Li PENG, Ctirad HOFR, Ronald EMESON a Frederic ALLAIN. The Solution Structure of the ADAR2 dsRBM-RNA Complex Reveals a Sequence-Specific Readout of the Minor Groove. CELL. UNITED STATES: CELL PRESS, 2010, roč. 143, č. 2, s. 225-237. ISSN 0092-8674.

PERGOLI, Roberto, Karel KUBÍČEK, Fruzsina HÓBOR, Josef PASULKA a Richard ŠTEFL. (1)H, (13)C, and (15)N chemical shift assignments for the RNA recognition motif of Nab3. Biomolecular NMR Assignments. UNITED STATES: SPRINGER, 2010, roč. 4, č. 1, s. 119-121. ISSN 1874-2718. Dostupné z: https://dx.doi.org/10.1007/s12104-010-9221-1.

SAŇUDO ARCE, Maria, Martin JACKO, Christiane RAMMELT, Štěpánka VAŇÁČOVÁ a Richard ŠTEFL. 1H, 13C, and 15N chemical shift assignments of ZCCHC9. Biomolecular NMR Assignments. SPRINGER, 2010, roč. 5, č. 1, s. 19-21. ISSN 1874-2718. Dostupné z: https://dx.doi.org/10.1007/s12104-010-9257-2.

ČERNÁ, Hana, Karel KUBÍČEK a Richard ŠTEFL. Recognition of phosphorylated CTD of RNA Pol II by Nrd1. In Recognition of phosphorylated CTD of RNA Pol II by Nrd1. 2009. ISSN 1211-5894.

HÓBOR, Fruzsina, Karel KUBÍČEK, Josef PASULKA a Richard ŠTEFL. Structure and RNA binding of Nab3. In Structure and RNA binding of Nab3. 2009. ISSN 1211-5894.

PASULKA, Josef, Jaroslav KOČA a Richard ŠTEFL. The molecular dynamics study of the RNA-binding domain of ADAR2 bound to dsRNA. In 7th Discussions in Structural Molecular Biology Nove Hrady, 12 - 14 March 2009. 2009. ISSN 1211-5894.

HÓBOR, Fruzsina, Hana ČERNÁ, Veronika BAČÍKOVÁ, Josef PASULKA, Karel KUBÍČEK a Richard ŠTEFL. Transcription termination of nonpolyadenylated transcripts. In Transcription termination of nonpolyadenylated transcripts. 2009. ISSN 1211-5894.

VAŇÁČOVÁ, Štěpánka a Richard ŠTEFL. The exosome and RNA quality control in the nucleus. EMBO REPORTS. Nature Publishing Group, London, UK: Nature Publishing Group, London, UK, 2007, roč. 8, č. 7, s. 651-657. ISSN 1469-221X.

SKRISOVSKA, Lenka, Cyril BOURGEOIS, Richard ŠTEFL, Sushma-Nagaraja GRELLSCHEID, Liliane KISTER, Philipp WENTER, David ELLIOTT, James STEVENIN a Frederic ALLAIN. The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction. EMBO REPORTS. Nature Publishing Group, London, UK: Nature Publishing Group, London, UK, 2007, roč. 8, č. 4, s. 372–379. ISSN 1469-221X.

ŠTEFL, Richard. "Lock and key" recognition in the world of protein-RNA interactions: How ADAR2 binds RNA. In xxx. Croatia: xxxx, 2006, s. 36.

ŠTEFL, Richard. "Lock and key" recognition in the world of protein-RNA interactions: How ADAR2 binds RNA. USA: xxx, 2006. xxx.

ŠTEFL, Richard. RNA recognition by the ADAR2 dsRBMs. In Meeting of Internationat Resarch Scholars. USA: Howard Hughes Medical Institute, 2006, s. 71-153.

OBERSTRASS, Florian, Albert LEE, Richard ŠTEFL, Michael JANIS, Guillaume CHANFREAU a Frederic ALLAIN. Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. NATURE STRUCTURAL & MOLECULAR BIOLOGY. 2006, roč. 13, č. 2, s. 160-167. ISSN 1545-9985.

STEFL, Richard, Ming XU, Lenka SKŘÍŠOVSKÁ, Ron EMESON a Frederic ALLAIN. Structure and Specific RNA Binding of ADAR2 Double-Stranded RNA Binding Motifs. Structure. 2006, roč. 14, č. 2, s. 345–355. ISSN 0969-2126.

ŠTEFL, Richard. Structure and specific RNA-binding of ADAR2 double-stranded RNA-binding motifs. Brno: Masaryk University, 2006.

ŠTEFL, Richard a Frederic ALLAIN. A novel RNA pentaloop fold involved in targeting ADAR2. RNA. 2005, roč. 11, č. 5, s. 592-597. ISSN 1355-8382.

ŠTEFL, Richard, Lenka SKŘÍŠOVSKÁ, Ming XU, Ron EMESON a Frederic ALLAIN. Resonance assignments of the double-stranded RNA-binding of adenosine deaminase acting on RNA 2 (ADAR2). JOURNAL OF BIOMOLECULAR NMR. 2005, roč. 31, č. 1, s. 71-72. ISSN 0925-2738.

ŠTEFL, Richard, Lenka SKŘÍŠOVSKÁ a Frederic ALLAIN. RNA sequence- and shape-dependent recognition by proteins in the ribonucleoprotein particle. EMBO REPORTS. 2005, roč. 6, č. 1, s. 33-38. ISSN 1469-221X.

ŠTEFL, Richard, Haihong WU, Sapna RAVINDRANATHAN, Vladimír SKLENÁŘ a Juli FEIGON. DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum. Proceedings of the National Academy of Sciences of the U.S.A. 2004, roč. 101, č. 5, s. 1171-1176. ISSN 0027-8424.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jaroslav KOČA, Thomas E. CHEATHAM a Jiří ŠPONER. Molecular dynamics simulations of guanine quadruplex loops:Advances and force field limitations. Biophysical Journal. Bethesda, USA: Biophysical Society, 2004, roč. 87, č. 1, s. 227-242. ISSN 0006-3495.

ŠTEFL, Richard, Thomas E. CHEATHAM, Naděžda ŠPAČKOVÁ, Eva FADRNÁ, Imre BERGER, Jaroslav KOČA a Jiří ŠPONER. Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamics Analysis of the Substates. Biophysical Journal. Bethesda, USA: Biophysical Society, 2003, roč. 85, č. 3, s. 1787-1804. ISSN 0006-3495.

ŠPAČKOVÁ, Naděžda, Richard ŠTEFL, Imre BERGER, Eva FADRNÁ, Jaroslav KOČA, T.E. CHEATHAM III a Jiří ŠPONER. Molecular Dynamics of Guanine Quadruplex Molecules. In Book of Abstracts. Albany, NY, USA: 13th Conversatin in the Discipline Biomolecular Structure and Dynamics, 2003, s. 001-1.

RÉBLOVÁ, Kamila, Nadezda SPACKOVÁ, Richard STEFL, Kristina CSASZAR, Jaroslav KOCA, Neocles LEONTIS a Jiri SPONER. Non-Watson-Crick Basepairing and Hydration in RNA Motifs:. Biophysical Journal. New York, USA: Rockefeller University, 2003, roč. 84, č. 6, s. 3564-3582, 18 s. ISSN 0006-3465.

TRANTÍREK, Lukáš, Richard ŠTEFL, James MASSE, Juli FEIGON a Vladimír SKLENÁŘ. Determination of the glycosidic torsion angels in uniformly C-13 labeled nucleic acids from vicinal coupling constants 3J(C2/4-H1') and 3J(C6/8-H1'). Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, 2002, roč. 23, č. 1, s. 1-12. ISSN 0925-2738.

RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Kristina CSASZAR, Jaroslav KOČA, Neocles LEONTIS a Jiří ŠPONER. Molecular dynamics of the 5S rRNA loop E. In Chemometrics. Brno: Chemometrics VI., 2002, s. 18-18.

PADRTA, Petr, Richard ŠTEFL, Lukáš KRÁLÍK, Lukáš ŽÍDEK a Vladimír SKLENÁŘ. Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings. Journal of Biomolecular NMR. Dordrecht: Kluwer/Escom, 2002, roč. 24, č. 1, s. 1-14. ISSN 0925-2738.

ŠTEFL, Richard, Lukáš TRANTÍREK, Michaela VORLÍČKOVÁ, Jaroslav KOČA, Vladimír SKLENÁŘ a Jaroslav KYPR. A-like Guanine-Guanine Stacking in the Aqueous DNA. Journal of Molecular Biology. USA: Academic Press, 2001, roč. 307, č. 1, s. 513-524. ISSN 0022-2836.

ŠTEFL, Richard, Naděžda ŠPAČKOVÁ, Imre BERGER, Jaroslav KOČA a Jiří ŠPONER. Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine. Biophysical Journal. Bethesda, USA: Biophysical Society, 2001, roč. 80, č. 1, s. 455-468. ISSN 0006-3495.

ŠTEFL, Richard, Naďa ŠPAČKOVÁ, Imre BERGER, Jaroslav KOČA a Jiří ŠPONER. Molecular Dynamics of DNA Quadruplex Molecules Containing Inosine, 6-Thioguanine and 6-Thiopurine. Biophysical Journal. New York, USA: Rockefeller University, 2001, roč. 80, č. 1, s. 455-468. ISSN 0006-3465.

CSASZAR, Kristina, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jiří ŠPONER a Neocles B. LEONTIS. Molecular dynamics of the frame-shifting pseudoknot from beet western yellows virus: The role of non- Watson-Crick base-pairing, ordered hydration, cation binding and base mutations on stability and unfolding. Journal of Molecular Biology. London: Academic Press, 2001, roč. 313, č. 5, s. 1073-1091. ISSN 0022-2836.

ŽÍDEK, Lukáš, Richard ŠTEFL a Vladimír SKLENÁŘ. NMR methodology for the study of nucleic acids. Current Opinion in Structural Biology. London: Elsevier Science Ltd., 2001, roč. 11, č. 3, s. 275-281. ISSN 0959-440X.

TRANTÍREK, Lukáš, Milan URBÁŠEK, Richard ŠTEFL, Juli FEIGON a Vladimír SKLENÁŘ. A Method for Direct Determination of Helical Parameters in Nucleic Acids Using Residual Dipolar Couplings. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2000, roč. 122, č. 42, s. 10454-10455. ISSN 0002-7863.

TRANTÍREK, Lukáš, Richard ŠTEFL, Michalea VORLÍČKOVÁ, Jaroslav KOČA, Vladimír SKLENÁŘ a Jaroslav KYPR. An A-type Double Helix of DNA Having B-type Puckering of the Deoxyribose Rings. Journal of Molecular Biology. USA: Academic Press, 2000, roč. 297, č. 4, s. 907-922. ISSN 0022-2836.

ŠTEFL, Richard a Jaroslav KOČA. Unrestrained Molecular Dynamics Simulations of d(AT5]2 Duplex in Aqueous Solution: Hydration and Sodium Ions Binding in the Minor Groove. Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 2000, roč. 122, č. 22, s. 5025-5033. ISSN 0002-7863.

ŠTEFL, Richard, Eva FADRNÁ a Jaroslav KOČA. Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 1999, roč. 16, č. 5, s. 1087-1095. ISSN 0739-1102.