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J

Jiřı́ Šponer

Czech Academy of Sciences

87H-index
641Paper Count
3.5WCitation Count
Published Papers 247
Publication Date
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Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking
errJournal of Chemical Theory and Computation
IF5.5
err2026-05-14
err0
errOAAI
errPetra Kührová; Vojtěch Mlýnský; Ivo Frébort; Jitka Frébortová; Michal Otyepka; Jiří Šponer; Pavel Banáš
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errSave
Newton’s cradle-like allosteric mechanism explains regulatory RsmE RNA binding
errNature Communications
IF15.7
err2026-04-22
err0
errOAAI
errEsteban Finol; Fred F. Damberger; Miroslav Krepl; Timo Flügel; Priscilla Dietrich; Thomas C. T. Michaels; Beat Vögeli; Jiří Šponer; Frédéric H-T. Allain
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errSave
Destabilization of Structured RNAs by OPC and TIP4PD Water Models
errJournal of Chemical Theory and Computation
IF5.5
err2026-02-01
err0
errOAAI
errKrepl, Miroslav; Mlynsky, Vojtech; Rusnakova, Agnesa; Banas, Pavel; Otyepka, Michal; Sponer, Jiri
errShare
errSave
Deciphering the intermolecular interactions between G-quadruplex (G4)-forming sequences
errNUCLEIC ACIDS RESEARCH
IF13.1
err2025-12-11
err0
errOAAI
errXia, Jianjun; Zhou, Jiahang; Zhuang, Xinzhe; Ju, Huangxian; Monchaud, David; Chaires, Jonathan B.; Sponer, Jiri; Mergny, Jean-Louis; Zhou, Jun
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errSave
The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2025-12-01
err0
PREAI
errLemmens, Toon; Mlynsky, Vojtech; Sponer, Jiri; Pykal, Martin; Banas, Pavel; Otyepka, Michal; Krepl, Miroslav
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errSave
Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2025-12-01
err0
PREAI
errNedelnikova, Andrea; Stadlbauer, Petr; Banas, Pavel; Sponer, Jiri; Otyepka, Michal; Kuhrova, Petra; Paloncyova, Marketa
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errSave
Structural basis of bis-quinolinium ligands binding to quadruplex-duplex hybrids from PIM1 oncogene
errNUCLEIC ACIDS RESEARCH
IF13.1
err2025-09-23
err0
PREAI
errGhosh, Anirban; Harnos, Jakub; Stadlbauer, Petr; Sponer, Jiri; Zivkovic, Martina Lenarcic; Trantirek, Lukas
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errSave
RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways
errNUCLEIC ACIDS RESEARCH
IF13.1
err2025-09-23
err0
PREAI
errPokorna, Pavlina; Mlynsky, Vojtech; Sponer, Jiri; Stadlbauer, Petr
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errSave
Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of the UUCG RNA Tetraloop and Other Systems
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2025-01-15
err0
errOAAI
errMlynsky, Vojtech; Kuhrova, Petra; Pykal, Martin; Krepl, Miroslav; Stadlbauer, Petr; Otyepka, Michal; Banas, Pavel; Sponer, Jiri
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errSave
How Binding Site Flexibility Promotes RNA Scanning by TbRGG2 RRM: A Molecular Dynamics Simulation Study
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2025-01-13
err0
errOAAI
errLemmens, Toon; Sponer, Jiri; Krepl, Miroslav
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errSave
Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2025-01-03
err1
errOAAI
errZgarbova, Marie; Sponer, Jiri; Jurecka, Petr
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errSave
The Drosophila RNA binding protein Hrp48 binds a specific RNA sequence of the msl-2 mRNA 3' UTR to regulate translation
errBIOPHYSICAL CHEMISTRY
IF2.2
err2025-01-01
err2
errOAAI
errLomoschitz, Andrea; Meyer, Julia; Guitart, Tanit; Krepl, Miroslav; Lapouge, Karine; Hayn, Clara; Schweimer, Kristian; Simon, Bernd; Sponer, Jiri; Gebauer, Fatima; Hennig, Janosch
errShare
errSave
Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space
errJOURNAL OF COMPUTATIONAL CHEMISTRY
IF4.8
err2024-12-09
err0
PREAI
errJanecek, Michal; Kuhrova, Petra; Mlynsky, Vojtech; Stadlbauer, Petr; Otyepka, Michal; Bussi, Giovanni; Sponer, Jiri; Banas, Pavel
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errSave
N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition
errNUCLEIC ACIDS RESEARCH
IF13.1
err2024-08-24
err1
errOAAI
errDamberger, Fred F.; Krepl, Miroslav; Arora, Rajika; Beusch, Irene; Maris, Christophe; Dorn, Georg; Sponer, Jiri; Ravindranathan, Sapna; Allain, Frederic H-T
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errSave
Phosphoric acid salts of amino acids as a source of oligopeptides on the early Earth
errCOMMUNICATIONS CHEMISTRY
IF6.2
err2024-08-22
err0
errOAAI
errSponer, Judit E.; Coulon, Remi; Otyepka, Michal; Sponer, Jiri; Siegle, Alexander F.; Trapp, Oliver; Slepokura, Katarzyna; Zdrahal, Zbynek; Sedo, Ondrej
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errSave
Comprehensive Assessment of Force-Field Performance in Molecular Dynamics Simulations of DNA/RNA Hybrid Duplexes
errJOURNAL OF CHEMICAL THEORY AND COMPUTATION
IF5.5
err2024-07-16
err6
errOAAI
errKnappeova, Barbora; Mlynsky, Vojtech; Pykal, Martin; Sponer, Jiri; Banas, Pavel; Otyepka, Michal; Krepl, Miroslav
errShare
errSave
Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes (vol 63, pg 2133, 2023)
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-06-27
err0
errOAAI
errKuhrova, Petra; Mlynsky, Vojtech; Otyepka, Michal; Sponer, Jiri; Banas, Pavel
errShare
errSave
Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3′-UTR of the SARS-CoV-2 genomic RNA
errNUCLEIC ACIDS RESEARCH
IF13.1
err2024-05-23
err2
errOAAI
errVoegele, Jennifer; Duchardt-Ferner, Elke; Bains, Jasleen Kaur; Knezic, Bozana; Wacker, Anna; Sich, Christian; Weigand, Julia E.; Sponer, Jiri; Schwalbe, Harald; Krepl, Miroslav; Woehnert, Jens
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errSave
Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations
errJOURNAL OF CHEMICAL INFORMATION AND MODELING
IF5.3
err2024-04-17
err0
errOAAI
errZhang, Zhengyue; Mlynsky, Vojtech; Krepl, Miroslav; Sponer, Jiri; Stadlbauer, Petr
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errSave
Molecular dynamics simulations reveal the parallel stranded d (GGGA)3GGG DNA quadruplex folds via multiple paths from a coil-like ensemble
errINTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
IF8.5
err2024-03-01
err2
errOAAI
errPokorna, Pavlina; Mlynsky, Vojtech; Bussi, Giovanni; Sponer, Jiri; Stadlbauer, Petr
errShare
errSave

Research Directions

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H-index: 115 · Papers: 704
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H-index: 112 · Papers: 573
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