Author

Petra Kührová

Czech Academy of Sciences, Institute of BiophysicsORCID 0000-0003-1593-5282Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Biophysics· 3

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Assay:multiome· 2 Approach:statistical model· 2 Approach:deep learning· 1 Approach:mechanistic / dynamical model· 1 Approach:simulation· 1

Frequent Co-Authors

Jiřı́ ŠponeriD· 3 shared Michal OtyepkaiD· 3 shared Pavel BanášiD· 3 shared Vojtěch MlýnskýiD· 3 shared Giovanni BussiiD· 1 shared Ivo FrébortiD· 1 shared Jitka FrébortováiD· 1 shared Martin PykaliD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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3 shared papersBiophysics

Jiřı́ ŠponerORCID

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3 papers

Recent·Most cited

BiophysicsJournal of Chemical Theory and ComputationPeer-reviewedAug 16, 2026

From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields

Vojtěch Mlýnský, Petra Kührová, Giovanni Bussi…·Pavel Banáš

This paper reparameterizes RNA force fields by replacing hydrogen-bond corrections with Lennard-Jones modifications, improving simulation accuracy without external potentials.

1 citation

multiomestatistical model

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BiophysicsJournal of Chemical Theory and ComputationPeer-reviewedMay 14, 2026

Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking

Petra Kührová, Vojtěch Mlýnský, Ivo Frébort…·Pavel Banáš

This study evaluates enhanced sampling methods for RNA force field benchmarking using an 8-mer tetraloop, finding T-REMD most robust for accurate folding free energy estimates.

DOI 10.1021/acs.jctc.6c00108

multiomedeep learning

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BiophysicsJournal of Chemical Theory and ComputationPeer-reviewedJan 15, 2025

Can We Ever Develop an Ideal RNA Force Field? Lessons Learned from Simulations of UUCG RNA Tetraloop and Other Systems.

Vojtěch Mlýnský, Petra Kührová, Martin Pykal…·Jiřı́ Šponer

This study evaluates RNA force fields using MD simulations of UUCG tetraloops, finding that some recent variants better preserve native structures but still show discrepancies in folding free energy estimates.

43 citationstop 1%

mechanistic / dynamical model

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