Jirí Sponer - researchr alias

researchr

You are not signed in
Sign in
Sign up

Viewing Publication 1 - 17 from 17

2025

Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational SpaceMichal Janecek, Petra Kührová, Vojtech Mlýnský, Petr Stadlbauer, Michal Otyepka, Giovanni Bussi, Jirí Sponer, Pavel Banás. jcc, 46(1), 2025. [doi]

How Binding Site Flexibility Promotes RNA Scanning by TbRGG2 RRM: A Molecular Dynamics Simulation StudyToon Lemmens, Jirí Sponer, Miroslav Krepl. jcisd, 65(2):896-907, 2025. [doi]

2024

Correction to "Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes"Petra Kührová, Vojtech Mlýnský, Michal Otyepka, Jirí Sponer, Pavel Banás. jcisd, 64(13):5356, 2024. [doi]

Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling SimulationsZhengyue Zhang, Vojtech Mlýnský, Miroslav Krepl, Jirí Sponer, Petr Stadlbauer. jcisd, 64(9):3896-3911, 2024. [doi]

2023

2022

A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building BlocksGabriele Amante, Judit E. Sponer, Jirí Sponer, Franz Saija, Giuseppe Cassone. entropy, 24(8):1012, 2022. [doi]

Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field DescriptionsKlaudia Mráziková, Holger Kruse, Vojtech Mlýnský, Pascal Auffinger, Jirí Sponer. jcisd, 62(23):6182-6200, 2022. [doi]

2021

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic AcidsKlaudia Mráziková, Jirí Sponer, Vojtech Mlýnský, Pascal Auffinger, Holger Kruse. jcisd, 61(11):5644-5657, 2021. [doi]

2019

Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis"Holger Kruse, Jirí Sponer, Pascal Auffinger. jcisd, 59(9):3605-3608, 2019. [doi]

2018

Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations studyAnna Bochicchio, Miroslav Krepl, Fan Yang, Gabriele Varani, Jirí Sponer, Paolo Carloni. ploscb, 14(12), 2018. [doi]

2017

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide SequencesMarie Zgarbová, Petr Jurecka, Filip Lankas, Thomas E. Cheatham III, Jirí Sponer, Michal Otyepka. jcisd, 57(2):275-287, 2017. [doi]

2013

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′, 5′-Cyclic GMPSamanta Pino, Giovanna Costanzo, Alessandra Giorgi, Jirí Sponer, Judit E. Sponer, Ernesto Di Mauro. entropy, 15(12):5362-5383, 2013. [doi]

1997

Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree-Fock resPavel Hobza, Martin Kabelác, Jirí Sponer, Petr Mejzlík, Jiri Vondrásek. jcc, 18(9):1136-1150, 1997. [doi]

1996

Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculationsJirí Sponer, Jerzy Leszczynski, Pavel Hobza. jcc, 17(7):841-850, 1996. [doi]

1995

Density Functional Theory and Moleculer ClustersPavel Hobza, Jirí Sponer, Tomas Reschel. jcc, 16(11):1315-1325, 1995.

Sign in or sign up to see more results.

runs on WebDSL