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Anatomy of enzyme channelsMOLE 2.0: advanced approach for analysis of biomacromolecular channelsMicrosecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies.Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations.The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists.Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.Free Energy Landscape of GAGA and UUCG RNA Tetraloops.Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs.Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field.Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics.Computer Folding of RNA Tetraloops? Are We There Yet?Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme.Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics.Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage.Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations.Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease.Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration.Exponential repulsion improves structural predictability of molecular docking.Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives.Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain IntactNoncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics SimulationsStructural dynamics of propeller loop: towards folding of RNA G-quadruplexInterplay between Ethanol Adsorption to High-Energy Sites and Clustering on Graphene and Graphite Alters the Measured Isosteric Adsorption EnthalpiesAre Waters around RNA More than Just a Solvent? – An Insight from Molecular Dynamics SimulationsMolecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the RibosomeThe nature of high surface energy sites in graphene and graphiteBenchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theoryEffect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration StudyNature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experimentConformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular MechanicsPerformance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins
P50
Q21146741-9D06BE2F-FA31-46D8-898D-D9BBF65FB075Q27703086-9B370577-9EA0-475E-905C-61A328660CCFQ31019657-E4DFC36A-B336-41A8-B715-85D43C697910Q33967967-F8EB9C59-575C-4718-A37B-34D0576EE326Q36225809-35DF79F5-97CB-41B7-B06B-D91687EC0204Q36422866-81F5D3D3-F720-4E87-8134-62C93E03BCBFQ36676471-BE6ACF61-E3DC-4B28-B96E-6C4D445ABFB5Q38052698-73F12C72-DC52-4D3E-B29F-6147B695AC3FQ38112952-7D4963CC-09F5-4C2B-959A-108BC5D44668Q38389887-54769221-4D52-4218-AB1B-CB9794D95145Q39013212-663BD6E7-A03A-421A-AE1C-DADA64736B41Q39354341-0DDAC17E-BEBF-4E78-9A83-8B95ABDA7B9BQ39358648-10A51EE9-5244-46DF-842E-6ED9559996A7Q40277136-8CC3F76E-7132-48B1-8020-DF3D59251CFBQ40294001-4ADEBE2D-0846-4314-B5D1-951DADBEE0F2Q40296196-DD25489D-71C4-4590-AF73-652960A94780Q40304238-BE916922-7DBC-45E9-9190-F9B6B2E8453CQ40308379-3C61C1D3-2696-40CE-AD78-CB964F261B8DQ40308953-25AD9398-CDA2-4FC6-93CD-B1EFAE2F46F2Q40315472-D8FAB44F-17D4-48D2-AFFA-BE5D8CE83C62Q41095160-6D8B6A9C-5922-44AB-8FE5-C16155FD5D1FQ41403588-9244BEE9-07FB-483D-9B0F-A3242879C3FCQ41755522-D3085308-2DA8-4DA5-A9F1-C2B1D7031F92Q41877122-575372A3-61F1-409A-B2F2-94D43CAC5D81Q42062129-F67E0398-F3F4-4F1B-972C-84EE6F37EFD7Q46979329-231C37EC-2810-4668-8C9C-0ABD8608953FQ51515408-4E7D8FB2-4B27-4AAD-BD71-B44BF5203472Q52925536-89656C38-AE16-482E-9C44-38249D7CB2E5Q56873342-FE74C91E-9C1B-4DC9-BE82-4875354F449AQ57539280-DB2B8E10-794F-40D7-AC79-B08E9FF11CD0Q57954714-906E5843-B26A-44B9-B622-4B95976C6CC9Q57954793-892C0051-1236-4933-8D3B-00B2EDDD44A9Q57954811-1158984C-2D27-46FD-AAEA-133A4EBB234FQ57954823-9A27A7F7-2907-4C13-929C-1BB4A63F9D58Q57954833-E65B1BE8-E2BE-48A2-9CB1-D071299D624CQ57954838-69DEBFD6-7429-4F60-8D27-5EFEF96578D3Q57954840-F8170836-0150-48C2-9AA4-F8E044AD9993Q57954845-7FFCF5F8-48D0-4FA6-8A41-C6D257F82BA0Q57954873-048A72AE-848B-4CEC-97C7-02E7E3BF0EF5Q57954877-A76DE70E-AB79-48ED-B06B-0BBAAC3436DB
P50
name
Pavel Banáš
@ast
Pavel Banáš
@en
Pavel Banáš
@nl
type
label
Pavel Banáš
@ast
Pavel Banáš
@en
Pavel Banáš
@nl
prefLabel
Pavel Banáš
@ast
Pavel Banáš
@en
Pavel Banáš
@nl