User profiles for Pavel Banáš
 | Pavel BanášCzech Advanced Technology and Research Institute CATRIN, Palacky University Olomouc Verified email at upol.cz Cited by 7309 |
Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force
field for RNA, χ OL . The parameters remove destabilization of the anti region found in the ff99 …
field for RNA, χ OL . The parameters remove destabilization of the anti region found in the ff99 …
[HTML][HTML] CAVER: a new tool to explore routes from protein clefts, pockets and cavities
Background The main aim of this study was to develop and implement an algorithm for the
rapid, accurate and automated identification of paths leading from buried protein clefts, …
rapid, accurate and automated identification of paths leading from buried protein clefts, …
RNA structural dynamics as captured by molecular simulations: a comprehensive overview
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to its …
pluripotent chemical species in molecular biology, and its functions are intimately linked to its …
Promoting transparency and reproducibility in enhanced molecular simulations
Molecular dynamics (MD) simulations have become an important tool for characterizing
mechanisms underlying complex processes, interpreting experimental measurements, and …
mechanisms underlying complex processes, interpreting experimental measurements, and …
Performance of molecular mechanics force fields for RNA simulations: stability of UUCG and GNRA hairpins
The RNA hairpin loops represent important RNA topologies with indispensable biological
functions in RNA folding and tertiary interactions. 5′-UNCG-3′ and 5′-GNRA-3′ RNA …
functions in RNA folding and tertiary interactions. 5′-UNCG-3′ and 5′-GNRA-3′ RNA …
[HTML][HTML] MOLE 2.0: advanced approach for analysis of biomacromolecular channels
Background Channels and pores in biomacromolecules (proteins, nucleic acids and their
complexes) play significant biological roles, eg, in molecular recognition and enzyme …
complexes) play significant biological roles, eg, in molecular recognition and enzyme …
Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA, and Z-DNA
Refinement of empirical force fields for nucleic acids requires their extensive testing using
as wide range of systems as possible. However, finding unambiguous reference data is not …
as wide range of systems as possible. However, finding unambiguous reference data is not …
Molecular dynamics simulations of nucleic acids. From tetranucleotides to the ribosome
J Šponer, P Banáš, P Jurecka… - The journal of …, 2014 - ACS Publications
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic
acids. We explain physical chemistry limitations of the simulations, namely, the molecular …
acids. We explain physical chemistry limitations of the simulations, namely, the molecular …
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels
Biomolecular channels play important roles in many biological systems, eg enzymes,
ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 …
ribosomes and ion channels. This article introduces a web-based interactive MOLEonline 2.0 …
Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment
…, JE Šponer, A Mládek, P Jurečka, P Banáš… - …, 2013 - Wiley Online Library
Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last
decades, base stacking has been extensively studied by experimental and theoretical …
decades, base stacking has been extensively studied by experimental and theoretical …