Structure and Dynamics of Nucleic Acids

Cassone, G., Creazzo, F., Giaquinta, PV., Saija, F., Saitta, AM. (2016), Ab initio molecular dynamics study of an aqueous NaCl solution under an electric field, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18, 23164-23173

Galindo-Murillo, R., Robertson, JC., Zgarbova, M., Sponer, J., Otyepka, M., Jurecka, P., Cheatham, TE. (2016), Assessing the Current State of Amber Force Field Modifications for DNA, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12, 4114-4127

Islam, B., Stadlbauer, P., Neidle, S., Haider, S., Sponer, J. (2016), Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds?, JOURNAL OF PHYSICAL CHEMISTRY B 120, 2899-2912

Kuhrova, P., Best, RB., Bottaro, S., Bussi, G., Sponer, J., Otyepka, M., Banas, P. (2016), Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12, 4534-4548

Gkionis, K., Kruse, H., Sponer, J. (2016), Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes, JOURNAL OF CHEMICAL THEORY AND COMPUTATION 12, 2000-2016

Sponer, JE., Sponer, J., Novakova, O., Brabec, V., Sedo, O., Zdrahal, Z., Costanzo, G., Pino, S., Saladino, R., Di Mauro, E. (2016), Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario, CHEMISTRY-A EUROPEAN JOURNAL 22, 3572-3586

Sponer, JE., Sponer, J., Di Mauro, E. (2016), Four Ways to Oligonucleotides Without Phosphoimidazolides, JOURNAL OF MOLECULAR EVOLUTION 82, 5-10

Rebic, M., Laaksonen, A., Sponer, J., Ulicny, J., Mocci, F. (2016), Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models, JOURNAL OF PHYSICAL CHEMISTRY B 120, 7380-7391

Drsata, T., Zgarbova, M., Jurecka, P., Sponer, J., Lankas, F. (2016), On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA, BIOPHYSICAL JOURNAL 110, 874-876

Sponer, JE., Szabla, R., Gora, RW., Saitta, AM., Pietrucci, F., Saija, F., Di Mauro, E., Saladino, R., Ferus, M., Civis, S., Sponer, J. (2016), Prebiotic synthesis of nucleic acids and their building blocks at the atomic level - merging models and mechanisms from advanced computations and experiments, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18, 20047-20066

Krepl, M., Clery, A., Blatter, M., Allain, FHT., Sponer, J. (2016), Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs, NUCLEIC ACIDS RESEARCH 44, 6452-6470

Civis, S., Szabla, R., Szyja, BM., Smykowski, D., Ivanek, O., Knizek, A., Kubelik, P., Sponer, J., Ferus, M., Sponer, JE. (2016), TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth, SCIENTIFIC REPORTS 6

Szabla, R., Gora, RW., Sponer, J. (2016), Ultrafast excited-state dynamics of isocytosine, PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18, 20208-20218