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Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.

A. Bochicchio, M. Krepl, F. Yang, G. Varani, J. Sponer, and P. Carloni. PLoS Comput. Biol., (2018)

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Jirí Mencák

Jirí Panyr

Jirí Friml

Jirí Simácek

Knut Sponer

Other publications of authors with the same name

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids.K. Mráziková, J. Sponer, V. Mlýnský, P. Auffinger, and H. Kruse. J. Chem. Inf. Model., 61 (11): 5644-5657 (2021)Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions.K. Mráziková, H. Kruse, V. Mlýnský, P. Auffinger, and J. Sponer. J. Chem. Inf. Model., 62 (23): 6182-6200 (2022)Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.M. Zgarbová, P. Jurecka, F. Lankas, T. III, J. Sponer, and M. Otyepka. J. Chem. Inf. Model., 57 (2): 275-287 (2017)Interactions of the "piano-stool" ruthenium(II) (eta6-arene)(en)CL+ complexes with water and nucleobases; ab initio and DFT study.Z. Futera, J. Klenko, J. Sponer, J. Sponer, and J. Burda. J. Comput. Chem., 30 (12): 1758-1770 (2009)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 results.P. Hobza, M. Kabelác, J. Sponer, P. Mejzlík, and J. Vondrásek. J. Comput. Chem., 18 (9): 1136-1150 (1997)Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.Z. Zhang, J. Sponer, G. Bussi, V. Mlýnský, P. Sulc, C. Simmons, N. Stephanopoulos, and M. Krepl. J. Chem. Inf. Model., 63 (9): 2794-2809 (May 2023)A Computational Quantum-Based Perspective on the Molecular Origins of Life's Building Blocks.G. Amante, J. Sponer, J. Sponer, F. Saija, and G. Cassone. Entropy, 24 (8): 1012 (2022)Molecular basis for the increased affinity of an RNA recognition motif with re-engineered specificity: A molecular dynamics and enhanced sampling simulations study.A. Bochicchio, M. Krepl, F. Yang, G. Varani, J. Sponer, and P. Carloni. PLoS Comput. Biol., (2018)Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′, 5′-Cyclic GMP.S. Pino, G. Costanzo, A. Giorgi, J. Sponer, J. Sponer, and E. Mauro. Entropy, 15 (12): 5362-5383 (2013)Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis".H. Kruse, J. Sponer, and P. Auffinger. J. Chem. Inf. Model., 59 (9): 3605-3608 (2019)

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Disambiguation of "Sponer, Jirí"