Publication Records

SVOZIL, Daniel, Judit SPONER, Ivan MARCHAN, Alberto PEREZ, Thomas CHEATHAM, Ferda FORTI, Javier LUQUE, Modesto OROZCO and Jiri SPONER. Geometrical and Electronic Structure Variability of the Sugar-phosphate Backbone in Nucleic Acids. Journal of Physical Chemistry B. 2008, vol. 112, No 27, p. 8188–8197. ISSN 1520-6106.

MISHRA, Navnit Kumar, Petr KULHÁNEK, Lenka ŠNAJDROVÁ, Martin PETŘEK, Anne IMBERTY and Jaroslav KOČA. Molecular dynamics study of Pseudomonas eruginosa lectin-II complexed with monosaccharides. Proteins: Structure, Function, and Bioinformatics. Wiley, 2008, vol. 72, No 1, p. 382–392. ISSN 0887-3585.

WIESNER, Jiří, Zdeněk KŘÍŽ and Jaroslav KOČA. Alternative entrances into the acetylcholinesterase active site. In Strukturní biofyzika makromolekul II. 2007.

MACEK, Pavel, Petr NOVÁK, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. Backbone Motions of Free and Pheromone-Bound Major Urinary Protein I Studied by Molecular Dynamics Simulation. Journal of Physical Chemistry B. USA: The American Chemical Society, 2007, vol. 111, No 20, p. 5731-5739. ISSN 1089-5639.

ŠPONER, Jiří. Computational studies of nucleic acids, advances and failures. In Modeling Interactions in Biomolecules III. Praha: Mff UK, Praha, 2007, p. 51.

RÁZGA, Filip, Jaroslav KOČA, Ali MOKDAD and Jiří ŠPONER. Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA. Nucleic Acids Research. Oxford, UK: Oxford Press, 2007, vol. 35, No 12, p. 4007–4017. ISSN 0305-1048.

RÁZGA, Filip, Jaroslav KOČA and Jiří ŠPONER. Elastic properties of ribosomal RNA building blocks: Molecular dynamics study. In Strukturní biofyzika makromolekul II. první. Brno: Brno, 2007, p. 14-14.

ŠPONER, Jiří. Molecular dynamics simulations of quadruplex DNA. In First international meeting on quadruplex DNA,. Louisville, USA: Louisville, USA, 2007, p. 20.

BERSHTEIN, Vladimir A., Larisa M. EGOROVA, Pavel N. YAKUSHEV, Vladimír ŠINDELÁŘ, Petr SYSEL, Tatiana E. SUKHANOVA, Irina P. DOBROVOLSKAYA, Anatoly I. GRIGORIEV, Sotiria KRIPOTOU and Polycarpos PISSIS. Poly(imide-amide)-poly(ethylene glycol) hybrid networks: nanostructure, molecular dynamics and membrane properties. Polymer Bulletin. Germany: Springer, 2007, vol. 58, No 1, p. 65-74. ISSN 0170-0839.

ŠPONER, Jiří, Ali MOKDAD, Filip RÁZGA, Kamila RÉBLOVÁ and Naděžda ŠPAČKOVÁ. Ribosomal RNA motifs and segments have salient flexibilities. In Journal Of Biomolecular Structure and Dynamics. prve. Albany: Adenine Press, 2007, p. 632-633. ISSN 0006-3525.

RÉBLOVÁ, Kamila, Filip LANKAS and Jiri SPONER. Study of structure, dynamics and local elasticity of 16S rRNA Helix 44 using molecular dynamics methods. In Journal Of Biomolecular Structure and Dynamics. prve. Albany: Adenine Press, 2007, p. 635-635. ISSN 0006-3525.

WIESNER, Jiří, Zdeněk KŘÍŽ and Jaroslav KOČA. Tryptophane as a Rotating Flap: Omega Loop Dynamics in Acetylcholinesterase. In Modeling Interactions in Biomolecules III. 2007.

SKLENÁŘ, Vladimír. Dynamics of Protein-Ligand Interactions. In Frontieres of Biomolecular NMR. Lubjlana: Narodna i univerzitetna knjižnica, Ljubljana, 2006, p. 41-41. ISBN 961-6104-08-X.

MATOUŠEK, Jiří, Petr KULHÁNEK, Michal ČAJAN and 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, vol. 110, No 3, p. 861-867. ISSN 1089-5639.

ŠPAČKOVÁ, Naděžda and Jiří ŠPONER. Molecular dynamics simulations of sarcin-ricin rRNA motif. Nucleic Acids Research. Oxford University Press, 2006, vol. 34, No 2, p. 697-708. ISSN 0006-3465.

MACEK, Pavel, Petr NOVÁK, Hana KŘÍŽOVÁ, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. Molecular dynamics study of major urinary protein-pheromone interactions: A structural model for ligand-induced flexibility increase. FEBS Letters. Amsterdam: Elsevier Science B.V., 2006, vol. 580, No 1, p. 682-684. ISSN 0014-5793.

SVOZIL, Dan, Jiří ŠPONER, Thomas E CHEATHAM and Modesto OROZCO. On the problem with long MD simulations of nucleic acids. In 2006 ISQBP president's meeting. Strasbourg: Strasbourg, 2006, p. 42-42.

NOVÁK, Petr, Pavel MACEK, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. PAIN: Program for Analysis of Internal motioN, An Application to MD Simulated Motions of Major Urinary Protein-I. Materials Structure in Chemistry, Biology, Physics and Technology. Praha, 2006, vol. 13, No 1, p. 31-31. ISSN 1211-5894.

RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA and Jiří ŠPONER. RNA kink-turns as molecular elbows: Hydration, cation binding, and large-scale dynamics. Structure. USA: CELL PRESS, 1100 MASSACHUSETTS AVE, CAMB, 2006, vol. 14, No 5, p. 825-835, 10 pp. ISSN 0969-2126.

MOKDAD, Ali, Maryna KRASOVSKA, Jiří ŠPONER and Neocles B. LEONTIS. Structural and evolutionary classification of G/U wobble basepairs in the ribosome. Nucleic Acids Research. Oxford University Press, 2006, vol. 34, No 5, p. 1326-1341. ISSN 0006-3465.

ŠPONER, Jiří. Structure and dynamics of functional RNAs: 3 microseconds of explicit solvent MD. In 2006 ISQBP president's meeting. Strasbourg: Strasbourg, 2006, p. 41-41.

RÉBLOVÁ, Kamila, Filip LANKAŠ, Filip RÁZGA, Maryna V KRASOVSKA, Jaroslav KOČA and Jiří ŠPONER. Structure, Dynamics, and Elasticity of Free 16S rRNA Helix 44 Studied by Molecular Dynamics Simulations. Biopolymers. USA: Wiley InterScience, 2006, vol. 82, No 5, p. 504-520. ISSN 0006-3525.

RHODES, Maria, Kamila REBLOVA, Walter NILS and Jiri SPONER. Trapped water molecules are essential to structural dynamics and function of a ribozyme. The Proceedings of the National Academy of Sciences. USA: National Academy of Sciences of the USA, 2006, vol. 103, No 36, p. 13380-13385. ISSN 1091-6490.

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY and Jaroslav KOČA. Computer Simulations on Glycosyltransferases Beauties and Pitfalls. In Eurocarb XIII. Bratislava: AV, 2005, p. 24-24.

OTYEPKA, Michal, Iveta BÁRTOVÁ, Zdeněk KŘÍŽ and Jaroslav KOČA. Dynamics of human CDK2 and CDK5 studied by computer simulations. In Cellular and Molecular Biology Letters. Wroclaw: Department of Genetic Biochemistry, Institute of Biochemistry, University of Wroclaw, 2005, p. 116-117. ISBN 1425-8153.

OTYEPKA, Michal, Iveta BÁRTOVÁ, Zdeněk KŘÍŽ and Jaroslav KOČA. Dynamika regulačních enzymů buněčných procesů CDK2 a CDK5 studovaná molekulovou dynamikou (Dynamics of human CDK2 and CDK5 studied by computer simulations). In ChemZi. Bratislava: Slovenská chemická spoločnosť, 2005, p. 277-277. ISBN 1336 - 7242.

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY and Jaroslav KOČA. Glycosyltransferase LgtC Active Site Hydration and Role of the Solvent in Substrate Binding. In Strukturní biofyzika makromolekul. Dubrovnik: ICS, 2005, p. 32-32.

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY and Jaroslav KOČA. Glycosyltransferase LgtC Active Site Hydration and Role of the Solvent in Substrate Binding. In Glycoproteomics - protein modifications for versatile functions. Dubrovnik: Dubrovnik, 2005, p. 62-62.

RÁZGA, Filip, Jaroslav KOČA, Jiří ŠPONER and Neocles B. LEONTIS. Hinge-Like Motions in RNA Kink-Turns: The Role of the Second A-minor Motif and Nominally Unpaired Bases. Biophysical Journal. USA: Biophysical Society, 2005, vol. 88, No 5, p. 3466-3485. ISSN 0006-3495.

FADRNÁ, Eva, Klára HLADEČKOVÁ and Jaroslav KOČA. Long-range Electrostatic Interactions in Molecular Dynamics: An Endothelin-1 Case Study. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 2005, vol. 23, No 2, p. 151-162. ISSN 0739-1102.

BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ and Jaroslav KOČA. Molecular Dynamics Simulations on Cyclin Dependent Kinase 2. Solvent Behavior Analysis and Activation and Inhibition by Phosphorylation -Tools to Design New Inhibitors and Contribute to Understanding Mechanism. In WATOC 2005. Modeling Structure and Reactivity. Cape Town: WATOC 2005., 2005, p. 83-83.

KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ and Jaroslav KOČA. Molecular Dynamics Study of Protein-Ligand Interactions. In Cellular and Molecular Biology Letters. Wroclaw: Department of Genetic Biochemistry, Institute of Biochemistry, University of Wroclaw, 2005, p. 111-112. ISBN 1425-8153.

WIESNER, Jiří, Zdeněk KŘÍŽ, Kamil KUČA, Daniel JUN and Jaroslav KOČA. Počítačové modelování a simulace - nové technologie při vývoji prostředkůproti chemickým bojovým látkám (Computer modeling and simulations - the new technologies in the development of means againts chemical warfare agents). Voj. zdrav. listy. Hradec Králové: Univerzita obrany, 2005, roč. 74, 5/6, p. 171-177. ISSN 0372-7025.

RÁZGA, Filip, Martin ZACHARIAS, Kamila RÉBLOVÁ, Jaroslav KOČA and Jiří ŠPONER. RNA Kink-Turns as Flexible Molecular Elbows Relevant to Ribosome Function. In Strukturní biofyzika makromolekul. prvé. Brno: Biofyzikálny ústav AVČR a MU v Brne, 2005, p. 17-17.

RÁZGA, Filip, Jaroslav KOČA, Neocles B LEONTIS and Jiří ŠPONER. RNA K-turns-Flexible Ribosomal Motifs:Dynamics, Hydration, Conformations and Biological Relevance. In Workshop on Modeling Interactions in Biomolecules II. prve. Praha: Praha, 2005, p. p37, 2 pp.

WIESNER, Jiří, Zdeněk KŘÍŽ and Jaroslav KOČA. Structure and dynamics of sarin-inhibited acetylcholinesterase. In Strukturní biofyzika makromolekul. Brno: Biofyzikálny ústav AVČR a MU v Brne, 2005, p. 21-21.

WIESNER, Jiří, Zdeněk KŘÍŽ and Jaroslav KOČA. Structure and dynamics of sarin-inhibited acetylcholinesterase. In Modeling Interactions in Biomolecules II. Praha: Univerzita Karlova, Praha, 2005, p. 1-1.

MATOUŠEK, Jiří, Petr KULHÁNEK, Michal ČAJAN and Jaroslav KOČA. The Role of Solvation in The Pinched Cone - Pinched Cone Interconversion. In Calix, 8th International Conference on Calixarenes. Praha: Institute of Chemical Technology Prague, 2005, p. P75, 1 pp.

BÁRTOVÁ, Iveta, Michal OTYEPKA, Zdeněk KŘÍŽ and Jaroslav KOČA. A Molecular Dynamics Study of the Cyclin-Dependent Kinase-2 (CDK2) with Substrate Peptide (HHASPRK), Inhibition of CDK2 by Phosphorylation. In Materials in Structure Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2004, p. 42-43. ISBN 1211 - 5894.

KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ and Jaroslav KOČA. Analysis of CDK2 active-site hydration: A method to design new inhibitors. Proteins: Structure, Function, and Bioinformatics. Wiley, 2004, vol. 55, No 3, p. 258-274. ISSN 0887-3585.

NOVÁK, Petr and Pavel MACEK. Analysis of Internal Motion from Molecular Dynamics of Major Urinary Protein I. Materials Structure. Praha: The Czech and Slovak Cryst. Assoc., 2004, vol. 11, No 1, p. 51-51. ISSN 1211-5894.

NOVÁK, Petr, Pavel MACEK, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. Analysis of Internal Motion from Molecular Dynamics of Major Urinary Protein I. In Abstract of the VIth Central European NMR Symposium. Linz: Institut fur Organische Chemie der Johannes Keppler Universitat, Linz, Austria, 2004, p. 20-20.

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY and Jaroslav KOČA. Computational Study of Galactosyltransferase LgtC in Complex with Manganese Ion and Donor Substrate. In Cukrblik 2004: Current Chemistry and Biochemistry of Saccharides. Praha: Ústav chemie přírodních látek VŠCHT, 2004, p. 6-6.

KŘÍŽ, Zdeněk, Michal OTYEPKA, Iveta BÁRTOVÁ and Jaroslav KOČA. Detailed study of interactions between small molecules and proteins using molecular modeling. In Materials in Structure Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2004, p. 47-47. ISBN 1211 - 5894.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER and Neocles B. LEONTIS. Dynamics of Flexible RNA Hinges Relevant to Ribosome Function: non-Watson-Crick basepairs, modular building and specific hydration of RNA Kink-turns. In Materials Structure in Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2004, p. 28. ISBN 1211-5894.

MATOUŠEK, Jiří, Michal ČAJAN, Petr KULHÁNEK and Jaroslav KOČA. Flexibility of Calix[4]arene Skeleton: A Molecular Dynamics Study. In Modelling and Design of Molecular Materials, Book of Abstracts. Wroclaw (Polsko): Wroclaw University of Technology, Poland, 2004, p. L-25, 1 pp.

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY and Jaroslav KOČA. Glycosyltransferase LgtC: MD Simulations under Physiological and Non-physiological Conditions (Glycosyltransferasa LgtC: MD Simulace). In 22nd International Carbohydrate Symposium. Glasgow: International Carbohydrate Organisation, 2004, p. P388, 1 pp.

MACEK, Pavel, Petr NOVÁK, Hana KŘÍŽOVÁ, Lukáš ŽÍDEK and Vladimír SKLENÁŘ. INCREASED DYNAMICS OF MUP-I IN PRESENCE OF LIGAND: EVIDENCE FROM MD SIMULATION AND NMR SPIN RELAXATION. In VIII. Pracovní setkání biochemiků a molekulárních biologů. Brno: Masarykova universita v Brně Přírodovědecká fakulta a Česká společnost pro biochemii a molekulární biologii, 2004, p. 31-31.

ŠNAJDROVÁ, Lenka, Anne IMBERTY, Petr KULHÁNEK and Jaroslav KOČA. MD Simulation of Glycosyltransferase LgtC in Water and in Solution of NaCl. In GlycoT 2004. Le Touquet, France: University of Lille, France, 2004, p. 117-117.

ŠNAJDROVÁ, Lenka, Petr KULHÁNEK, Anne IMBERTY and Jaroslav KOČA. Molecular dynamics simulations of glycosyltransferase LgtC. Carbohydrate Research. 2004, vol. 339, No 5, p. 995-1006. ISSN 0008-6215.

FADRNÁ, Eva, Naděžda ŠPAČKOVÁ, Richard ŠTEFL, Jaroslav KOČA, Thomas E. CHEATHAM and Jiří ŠPONER. Molecular dynamics simulations of guanine quadruplex loops:Advances and force field limitations. Biophysical Journal. Bethesda, USA: Biophysical Society, 2004, vol. 87, No 1, p. 227-242. ISSN 0006-3495.

ŠNAJDROVÁ, Lenka, Jaroslav KOČA and Anne IMBERTY. Molecular Dynamics Simulations on Glycosyltrasferase LgtC. In Materials Structure in Chemistry. Praha: Czech and Slovak Crystallographic Association, 2004, p. 52-52.

RÁZGA, Filip, Naďa ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Neocles B. LEONTIS and Jiří ŠPONER. Ribosomal RNA Kink-turn Motif - A Flexible Molecular Hinge. Journal of Biomolecular Structure & Dynamics. Adenine Press, 2004, vol. 22, No 2, p. 183-193. ISSN 0739-1102.

KOČA, Jaroslav. Are Force Fields Able to Predict Coordination Number of Metal Ions in Metalloproteins. In Modeling Interactions in Biomolecules, Workshop. Nove Hrady: Praha, 2003, p. 31-31.

FADRNÁ, Eva and Jaroslav KOČA. Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search. Journal of Biomolecular Structure and Dynamics. USA: Adenine Press, 2003, vol. 20, No 5, p. 715-731. ISSN 0739-1102.

KOČA, Jaroslav, Chang-Guo ZHAN, Robert RITTENHOUSE and Rick ORNSTEIN. Coordination number of zinc ions in the phosphotriesterase active site by molecular dynamics and quantum mechanics. Journal of Computational Chemistry. New York: John Wiley & Sons, 2003, vol. 24, No 3, p. 368-378. ISSN 0192-8651.

ŠTEFL, Richard, Thomas E. CHEATHAM, Naděžda ŠPAČKOVÁ, Eva FADRNÁ, Imre BERGER, Jaroslav KOČA and 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, vol. 85, No 3, p. 1787-1804. ISSN 0006-3495.

RÉBLOVÁ, Kamila, Naděžda ŠPAČKOVÁ, Judit ŠPONER, Jaroslav KOČA and Jiři ŠPONER. Molecular dynamics simulations of RNA kissing loop motifs reveal structural dynamics and formation of cation-binding pockets. Nucleic Acids Research. Oxford University Press, 2003, vol. 31, No 23, p. 6942-6952. ISSN 0006-3465.

ŠNAJDROVÁ, Lenka, Jaroslav KOČA and Anne IMBERTY. Molecular dynamics simulations on glycosyltransferase LgtC. In 12th European Carbohydrate Symposium. Grenoble: CERMAV-CNRS, 2003, p. 398-398.

LEPŠÍK, Martin, Zdeněk KŘÍŽ and Zdeněk HAVLAS. Nanosecond molecular dynamics of HIV protease-inhibitor complexes: Insight into the differential binding potency of diastereoisomers. In Materials in Structure Chemistry, Biology, Physics and Technology. Praha: Krystalografická společnost, 2003, p. 23-23. ISBN 1211 - 5894.

TRANTÍREK, Lukáš, Erik CAHA and Radovan FIALA. NMR Relaxation Studies of Fast Internal Motions in Nucleic Acids. In Materials Structure. 1st ed. Prague: Czech and Slovak Crystalographic Association, 2003, p. 40-41. ISBN 1211-5894.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER and Neocles, B. LEONTIS. Structure and Dynamics of RNA K-turn Motifs. In RNA klub. vyd. Praha: Praha, 2003, p. 21-21.

RÁZGA, Filip, Naděžda ŠPAČKOVÁ, Kamila RÉBLOVÁ, Jaroslav KOČA, Jiří ŠPONER and Neocles, B LEONTIS. Structure And Dynamics Of RNA K-Turn Motifs. In Workshop on Modeling Interactions in Biomolecules : Programme and Book of Abstract. vyd. Praha: Praha, 2003, p. 41-41.

OTYEPKA, Michal, Zdeněk KŘÍŽ and Jaroslav KOČA. Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations. Journal of Biomolecular Structure & Dynamics. GUILDERLAND: ADENINE PRESS, 2002, vol. 20, No 2, p. 141-154. ISSN 0739-1102.

OTYEPKA, Michal and Jiří DAMBORSKÝ. Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains. Protein Science. 2002, vol. 11, No 5, p. 1206-1217. ISSN 0961-8368.

KŘÍŽ, Zdeněk, Michal OTYEPKA and Jaroslav KOČA. Hydratace aktivniho mista enzymu CDK2. Studium pomoci molekulove dynamiky. (Hydration of the CDK2 active site. Molecular dynamics study.). In Chemicke listy 6. Praha: 54. Sjezd chemickych spolecnosti, 2002, p. 424.

KŘÍŽ, Zdeněk, Michal OTYEPKA and Jaroslav KOČA. Hydration of the CDK2 active site. Molecular dynamics study. In Watoc'02 Book of Abstracts. ETH Zurich: WATOC'02, 2002, p. PC439, 1 pp.

BÁRTOVÁ, Iveta, Zdeněk KŘÍŽ, Michal OTYEPKA and Jaroslav KOČA. Molecular Dynamics Simulations of CDK2/ATP Complex. In Chemicke listy 6. Praha: 54. Sjezd chemickych spolecnosti, 2002, p. 427.

KŘÍŽ, Zdeněk, Michal OTYEPKA and Jaroslav KOČA. Molecular Modeling of Peptides and Proteins at National Centre for Biomolecular Research (NCBR). In Materials Structure in Chemistry, Biology, Physics and Technology. Praha: 1. setkani ceskych a slovenskych strukturnich biologu, 2002, p. 41-42.

PETROVÁ, Pavla, Celine MONTEIRO, Catherine HERVE DU PENHOAT, Jaroslav KOČA and Anne IMBERTY. Conformational behavior of nucleotide-sugar in solution: Molecular dynamics and NMR study of solvated uridinediphosphate-glucose in the presence of monovalent cations. Biopolymers. John Wiley & Sons, Inc, 2001, vol. 58, No 7, p. 617-635. ISSN 0006-3525.

PETROVÁ, Pavla, Jaroslav KOČA and Anne IMBERTY. Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-glucose. (Effect of Cation Concentration on Molecular Dynamics Simulations of UDP-glucose). Molecular Simulations. 2000, vol. 24, No 1, p. 325-330.

ŠPAČKOVÁ, Naděžda, Imre BERGER and Jiří ŠPONER. Molecular Dynamics Simulations of Four-stranded Nucleic Acid Structures: i-DNA and G-DNA. In Biochemistry and molecular biology an the threshold of a new century. 1st ed. Brno: Masarykova univerzita, 2000, p. 90. ISBN 80-210-2266-3.

ŠPAČKOVÁ, Naděžda, Imre BERGER and Jiří ŠPONER. Nanosecond molecular dynamics simulations of parallel and antiparallel guanine quadruplex DNA molecules. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 1999, roč. 121, No 23, p. 5519-5534. ISSN 0002-7863.

ŠPAČKOVÁ, Naděžda, Imre BERGER, Martin EGLI and Jiří ŠPONER. Molecular Dynamics of Hemiprotonated Intercalated Four-stranded i-DNA and Guanine Quartets. Stable Trajectories on a Nanosecond Scale. Materials Structure. Praha: The Czech and Slovak Cryst. Assoc., 1998, vol. 5, p. 420. ISSN 1211-5894.

ŠPAČKOVÁ, Naděžda, Imre BERGER, Martin EGLI and Jiří ŠPONER. Molecular dynamics of hemiprotonated intercalated four-stranded i-DNA: stable trajectories on a nanosecond scale. The Journal of the American Chemical Society. Washington, D.C.: American Chemical Society, 1998, roč. 120, No 24, p. 6147-6151. ISSN 0002-7863.