List of works by Jirí Sponer

A G-quadruplex-binding compound showing anti-tumour activity in an in vivo model for pancreatic cancer

scientific article published on 16 June 2015

A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

scientific article published on 21 August 2012

A Systematic ab Initio Study of the Hydration of Selected Palladium Square-Planar Complexes. A Comparison with Platinum Analogues

scientific article published in August 2001

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

scientific article

A- to B-DNA Transition in AMBER Force Fields and Its Coupling to Sugar Pucker

scientific article published on 5 December 2017

A-Minor Tertiary Interactions in RNA Kink-Turns. Molecular Dynamics and Quantum Chemical Analysis

scientific article published in December 2011

Ab Initio Study of the Interaction of Guanine and Adenine with Various Mono- and Bivalent Metal Cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+)

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

scientific article published on 01 August 2004

Amino groups in nucleic acid bases, aniline, aminopyridines, and aminotriazine are nonplanar: Results of correlatedabinitioquantum chemical calculations and anharmonic analysis of the aniline inversion motion

scientific article published on 22 December 1996

An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods

scientific article

An intricate balance of hydrogen bonding, ion atmosphere and dynamics facilitates a seamless uracil to cytosine substitution in the U-turn of the neomycin-sensing riboswitch

scientific article published on 01 July 2018

Are Waters around RNA More than Just a Solvent? – An Insight from Molecular Dynamics Simulations

article

Are the hydrogen bonds of RNA (AU) stronger than those of DNA (AT)? A quantum mechanics study.

scientific article published in August 2005

Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations.

scientific article published on January 2000

Aromatic side-chain conformational switch on the surface of the RNA Recognition Motif enables RNA discrimination

scientific article published on 21 September 2017

Arsenic-nucleotides interactions: an experimental and computational investigation

scientific article published on 25 April 2020

Assessing the Current State of Amber Force Field Modifications for DNA

scientific article

Automatic Learning of Hydrogen-Bond Fixes in the AMBER RNA Force Field

scientific article published on 14 June 2022

Balance of Attraction and Repulsion in Nucleic-Acid Base Stacking: CCSD(T)/Complete-Basis-Set-Limit Calculations on Uracil Dimer and a Comparison with the Force-Field Description

scientific article published on 29 April 2009

Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA.

scientific article published on August 2014

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs

article

Benchmark quantum-chemical calculations on a complete set of rotameric families of the DNA sugar–phosphate backbone and their comparison with modern density functional theory

article by Arnošt Mládek et al published 2013 in Physical Chemistry Chemical Physics

Bifurcated hydrogen bonds in DNA crystal structures. An ab initio quantum chemical study

article by Jirí Sponer & Pavel Hobza published January 1994 in Journal of the American Chemical Society

Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops

article

Can We Accurately Describe the Structure of Adenine Tracts in B-DNA? Reference Quantum-Chemical Computations Reveal Overstabilization of Stacking by Molecular Mechanics

scientific article published on 6 June 2012

Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds?

scientific article

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

scientific article published on 3 February 2015

Cation binding to 15-TBA quadruplex DNA is a multiple-pathway cation-dependent process.

scientific article

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme

scientific article

Cation—π and Amino-Acceptor Interactions Between Hydrated Metal Cations and DNA Bases. A Quantum-Chemical View

scientific article published in June 2000

Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage

scientific article published on October 2015

Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment

scientific article published on 16 August 2012

Close mutual contacts of the amino groups in DNA

scientific article published in February 1994

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.

scientific article published on 21 October 2016

Combining NMR Spectroscopy and Molecular Dynamic Simulations to Solve and Analyze the Structure of Protein-RNA Complexes

scientific article published on 10 December 2018

Comment on "Evaluating Unexpectedly Short Non-covalent Distances in X-ray Crystal Structures of Proteins with Electronic Structure Analysis"

scientific article published on 19 August 2019

Comment on “Computational Model for Predicting Experimental RNA and DNA Nearest-Neighbor Free Energy Rankings”

scientific article published on 11 July 2012

Comment on “Electron-Correlated Calculations of Electric Properties of Nucleic Acid Bases”

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective.

scientific article

Comparison of Intrinsic Stacking Energies of Ten Unique Dinucleotide Steps in A-RNA and B-DNA Duplexes. Can We Determine Correct Order of Stability by Quantum-Chemical Calculations?

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

scientific article published on April 2014

Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?

scientific article

Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation

scientific article published on 31 March 2020

Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies.

scientific article published on 20 July 2016

Computer Folding of RNA Tetraloops? Are We There Yet?

scientific article published on 7 March 2013

Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics

article by Arnošt Mládek et al published 14 December 2010 in Journal of Chemical Theory and Computation

Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site

scientific article published on 03 March 2015

Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale.

scientific article

Conformational transitions of flanking purines in HIV-1 RNA dimerization initiation site kissing complexes studied by CHARMM explicit solvent molecular dynamics.

scientific article published in September 2008

Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics

scientific article

Coordination between the polymerase and RNase H activity of HIV-1 reverse transcriptase

scientific article

Correction to "Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions"

scientific article published on 19 December 2019

Correction to “Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes”

scientific article published on 20 February 2018

Correction to “Free Energy Landscape of GAGA and UUCG RNA Tetraloops”

scientific article published on 19 March 2018

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution : Part 1. Cytosine

Corrigendum: TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth

scientific article published on 20 June 2016

Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

scientific article

C−H···O Contacts in the Adenine···Uracil Watson−Crick and Uracil···Uracil Nucleic Acid Base Pairs: Nonempirical ab Initio Study with Inclusion of Electron Correlation Effects

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations ⬇️

scientific article published on November 1, 2003

Dependence of A-RNA simulations on the choice of the force field and salt strength

Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes

scientific article published on 8 March 2016

Different intrastrand and interstrand contributions to stacking account for roll variations at the alternating purine-pyrimidine sequences in A-DNA and A-RNA

scientific article published in October 1991

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

scientific article

Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM

scientific article

Effect of Guanine to Inosine Substitution on Stability of Canonical DNA and RNA Duplexes: Molecular Dynamics Thermodynamics Integration Study

article

Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes

scientific article published on 28 June 2017

Effect of local sugar and base geometry on 13C and 15N magnetic shielding anisotropy in DNA nucleosides

scientific article

Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs

scientific article

Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA

scientific article published on 6 June 2007

Elbow flexibility of the kt38 RNA kink-turn motif investigated by free-energy molecular dynamics simulations

scientific article published on October 2009

Electric-Field-Induced Effects on the Dipole Moment and Vibrational Modes of the Centrosymmetric Indigo Molecule

scientific article published on 11 December 2020

Electron-Driven Proton Transfer Along H2O Wires Enables Photorelaxation of πσ* States in Chromophore-Water Clusters.

scientific article published on 6 April 2015

Electron-driven proton transfer enables nonradiative photodeactivation in microhydrated 2-aminoimidazole

scientific article published on 01 December 2018

Emergence of the First Catalytic Oligonucleotides in a Formamide-Based Origin Scenario

scientific article

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

scientific article published on 22 November 2013

Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes

scientific article

Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.

scientific article

Extended molecular dynamics of a c-kit promoter quadruplex

scientific article

Fitting Corrections to an RNA Force Field Using Experimental Data

scientific article published on 23 May 2019

Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies

scientific article

Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates

scientific article

Four Ways to Oligonucleotides Without Phosphoimidazolides

scientific article

Free Energy Landscape of GAGA and UUCG RNA Tetraloops ⬇️

scientific article published on 23 September 2016

Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids

scientific article

Global Minimum of the Adenine···Thymine Base Pair Corresponds Neither to Watson−Crick Nor to Hoogsteen Structures. Molecular Dynamic/Quenching/AMBER and ab Initio beyond Hartree−Fock Studies

scientific article published in 2000

H-Bonded and Stacked DNA Base Pairs: Cytosine Dimer. An Ab Initio Second-Order Moeller-Plesset Study

article by Pavel Hobza et al published January 1995 in Journal of the American Chemical Society

Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations

scientific article published on 3 October 2015

High-energy chemistry of formamide: a simpler way for nucleobase formation

scientific article published on 17 January 2014

High-energy chemistry of formamide: a unified mechanism of nucleobase formation

scientific article

Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

scientific article

How Nucleobases Rotate When Bonded to a Metal Ion: Detailed View from an Ab Initio Quantum Chemical Study of a Cytosine Complex oftrans-a2PtII

scientific article published in December 2001

How does hydroxyl introduction influence the double helical structure: the stabilization of an altritol nucleic acid:ribonucleic acid duplex

scientific article

How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?

scientific article published on 10 November 2016

How to understand quantum chemical computations on DNA and RNA systems? A practical guide for non-specialists

scientific article published on 07 June 2013

Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies.

scientific article published on August 1996

Hydrogen bonding, stacking and cation binding of DNA bases

Hydrogen-bonded Trimers of DNA Bases and their Interaction with Metal Cations: Ab initio Quantum-chemical and Empirical Potential Study

scientific article published in April 1997

Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme.

scientific article published in April 2007

Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions

scientific article published on 02 April 2019

Indirect NMR Spin−Spin Coupling Constants3J(P,C) and2J(P,H) across the P−O···H−C Link Can Be Used for Structure Determination of Nucleic Acids

scientific article published in May 2006

Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences.

scientific article published on 06 January 2017

Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis

scientific article published on 19 August 2011

Insights into G-Quadruplex–Hemin Dynamics Using Atomistic Simulations: Implications for Reactivity and Folding

scientific article published on 06 February 2021

Insights into Stability and Folding of GNRA and UNCG Tetraloops Revealed by Microsecond Molecular Dynamics and Well-Tempered Metadynamics

scientific article published on August 2015

Interaction Energies of Hydrogen-Bonded Formamide Dimer, Formamidine Dimer, and Selected DNA Base Pairs Obtained with Large Basis Sets of Atomic Orbitals

article published in 2000

Interaction between As(III) and Simple Thioacids in Water: An Experimental and ab Initio Molecular Dynamics Investigation

scientific article published on 05 July 2019

Interaction between the Guanine−Cytosine Watson−Crick DNA Base Pair and Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and Group IIb (Zn2+, Cd2+, Hg2+) Metal Cations

Interaction of DNA Base Pairs with Various Metal Cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab Initio Calculations on Structures, Energies, and Nonadditivity of the Interaction

Interaction of the Adenine−Thymine Watson−Crick and Adenine−Adenine Reverse-Hoogsteen DNA Base Pairs with Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and IIb (Zn2+, Cd2+, Hg2+) Metal Cations: Absence of the Base Pair Stabilization by Metal-Indu

Interactions Between Amino Groups in DNA. An Ab Initio Study and a Comparison with Empirical Potentials

scientific article published in June 1994

Interactions of Hydrated IIa and IIb Group Metal Cations with Thioguanine-Cytosine DNA Base Pair: Ab initio and Density Functional Theory Investigation of Polarization Effects, Differences Among Cations, and Flexibility of the Cation Hydration Shell

scientific article published in August 1999

Interactions of Hydrated Mg2+Cation with Bases, Base Pairs, and Nucleotides. Electron Topology, Natural Bond Orbital, Electrostatic, and Vibrational Study

article

Interactions of hydrated divalent metal cations with nucleic acid bases. How to relate the gas phase data to solution situation and binding selectivity in nucleic acids

Intercalators. 1. Nature of Stacking Interactions between Intercalators (Ethidium, Daunomycin, Ellipticine, and 4‘,6‘-Diaminide-2-phenylindole) and DNA Base Pairs. Ab Initio Quantum Chemical, Density Functional Theory, and Empirical Potential Study

scientific article published in 2003

Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study

scientific article published in April 2002

Investigations of Stacked DNA Base-Pair Steps: Highly Accurate Stacking Interaction Energies, Energy Decomposition, and Many-Body Stacking Effects

scientific article published on 12 December 2018

Ion Binding to Quadruplex DNA Stems. Comparison of MM and QM Descriptions Reveals Sizable Polarization Effects Not Included in Contemporary Simulations

scientific article published on 01 March 2014

Ionic diffusion and proton transfer in aqueous solutions of alkali metal salts.

scientific article published on 24 July 2017

Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop

scientific article

Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations

article published in 2010

Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch

scientific article published on 20 September 2019

Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex

scientific article

Loss of Hoogsteen pairing ability upon N1 adenine platinum binding

scientific article published in June 2002

MD and QM/MM Study of the Quaternary HutP Homohexamer Complex with mRNA, l-Histidine Ligand, and Mg2.

scientific article published on 16 October 2017

Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis.

scientific article published on 8 November 2017

Mechanical Model of DNA Allostery

scientific article published on 21 October 2014

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning.

scientific article published on 14 May 2014

Mechanism of polypurine tract primer generation by HIV-1 reverse transcriptase

scientific article published on 9 November 2017

Metal ions in non-complementary DNA base pairs: an ab initio study of Cu(I), Ag(I), and Au(I) complexes with the cytosine-adenine base pair

scholarly article

Metal-Stabilized Rare Tautomers and Mispairs of DNA Bases: N6-Metalated Adenine and N4-Metalated Cytosine, Theoretical and Experimental Views

scientific article published in December 1999

Metal-mediated deamination of cytosine: experiment and DFT calculations

scientific article published in October 2004

Microsecond-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

scientific article

Mobilities of iodide anions in aqueous solutions for applications in natural dye-sensitized solar cells

scientific article published in 2018

Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models

scientific article published on 5 July 2016

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

article

Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies

article

Molecular basis for AU-rich element recognition and dimerization by the HuR C-terminal RRM

scientific article published on 04 February 2019

Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

scientific article published on 24 October 2014

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in

scientific article published on January 2010

Molecular dynamics of DNA quadruplex molecules containing inosine, 6-thioguanine and 6-thiopurine.

scientific article

Molecular dynamics simulations and their application to four-stranded DNA.

scientific article published on December 2007

Molecular dynamics simulations and thermodynamics analysis of DNA-drug complexes. Minor groove binding between 4',6-diamidino-2-phenylindole and DNA duplexes in solution

scientific article

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

scientific article

Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations

scientific article

Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets

scientific article

Molecular dynamics simulations of RNA: an in silico single molecule approach.

scientific article

Molecular dynamics simulations of sarcin-ricin rRNA motif.

scientific article

Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome

scientific article

Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.

scientific article published on 17 February 2009

Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study

scientific article published on 12 October 2012

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch

scientific article published in October 2017

NMR Cross-Correlated Relaxation Rates Reveal Ion Coordination Sites in DNA

scientific article published on 7 September 2011

Nanosecond Molecular Dynamics Simulations of Parallel and Antiparallel Guanine Quadruplex DNA Molecules

scientific article published in June 1999

Nanosecond Molecular Dynamics of Zipper-like DNA Duplex Structures Containing Sheared G·A Mismatch Pairs

scientific article published in August 2000

Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics and experiment

scientific article published in June 2013

Nature and magnitude of aromatic stacking of nucleic acid bases

scientific article published on 07 April 2008

Nature of Base Stacking: Reference Quantum-Chemical Stacking Energies in Ten Unique B-DNA Base-Pair Steps

scientific article published on 01 March 2006

Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs

New evolutionary insights into the non-enzymatic origin of RNA oligomers

scientific article

Non-Enzymatic Oligomerization of 3', 5' Cyclic AMP

scientific article

Non-Watson−Crick Base Pairing in RNA. Quantum Chemical Analysis of the cis Watson−Crick/Sugar Edge Base Pair Family

scientific article published in March 2005

Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

article

Noncanonical α/γ Backbone Conformations in RNA and the Accuracy of Their Description by the AMBER Force Field

scientific article published on 14 March 2017

Nonempirical ab initio calculations on DNA base pairs

Nonplanar DNA Base Pairs

scientific article published in April 1996

On the Geometry and Electronic Structure of the As-DNA Backbone

On the Role of cis Hoogsteen:Sugar Edge Family of Base Pairs in Platforms and Triplets—Quantum Chemical Insights into RNA Structural Biology

On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA.

scientific article published on 27 January 2016

On the potential role of the amino nitrogen atom as a hydrogen bond acceptor in macromolecules.

scientific article published in June 1998

On the road from formamide ices to nucleobases: IR-spectroscopic observation of a direct reaction between cyano radicals and formamide in a high-energy impact event

scientific article

Outer-Shell and Inner-Shell Coordination of Phosphate Group to Hydrated Metal Ions (Mg2+, Cu2+, Zn2+, Cd2+) in the Presence and Absence of Nucleobase. The Role of Nonelectrostatic Effects

scientific article published in February 2003

Performance of Molecular Mechanics Force Fields for RNA Simulations: Stability of UUCG and GNRA Hairpins

Photochemistry of 2-Aminooxazole, a Hypothetical Prebiotic Precursor of RNA Nucleotides

scientific article published on 6 August 2013

Photorelaxation of imidazole and adenine via electron-driven proton transfer along H2O wires

scientific article published on 3 October 2016

Potential Energy Surface of the Cytosine Dimer: MP2 Complete Basis Set Limit Interaction Energies, CCSD(T) Correction Term, and Comparison with the AMBER Force Field

Principles of RNA Base Pairing: Structures and Energies of the Trans Watson−Crick/Sugar Edge Base Pairs

scientific article published in June 2005

Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture

scientific article published in July 2001

QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin-Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches

scientific article published on 6 May 2014

QM/MM Calculations on Protein-RNA Complexes: Understanding Limitations of Classical MD Simulations and Search for Reliable Cost-Effective QM Methods

scientific article published on 24 September 2018

QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms

scientific article published on 8 November 2011

Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit.

scientific article published on 15 September 2015

Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?

scientific article (publication date: 9 December 2010)

RNA Kink-Turns as Molecular Elbows: Hydration, Cation Binding, and Large-Scale Dynamics

article

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

scientific article published on 3 January 2018

Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations

scientific article published on 5 March 2015

Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions

scientific article published on 12 February 2010

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

scientific article (publication date: June 2007)

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

article by Marie Zgarbová et al published 20 November 2015 in Journal of Chemical Theory and Computation

Relationships among Rise, Cup, Roll and Stagger in DNA Suggested by Empirical Potential Studies of Base Stacking

scientific article published in August 1993

Relative stability of different DNA guanine quadruplex stem topologies derived using large-scale quantum-chemical computations

scientific article published on 19 June 2013

Removal of As(III) from Biological Fluids: Mono- versus Dithiolic Ligands

scientific article published on 24 March 2020

Reverse Watson−Crick Isocytosine−Cytosine and Guanine−Cytosine Base Pairs Stabilized by the Formation of the Minor Tautomers of Bases. An ab Initio Study in the Gas Phase and in a Water Cluster

scientific article published in December 1998

Revisiting the Potential Energy Surface of the Stacked Cytosine Dimer: FNO-CCSD(T) Interaction Energies, SAPT Decompositions, and Benchmarking

scientific article published on 09 October 2019

Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion.

scientific article published on November 2009

Rewarming the Primordial Soup: Revisitations and Rediscoveries in Prebiotic Chemistry.

scientific article

Ribosomal RNA Kink-turn Motif—A Flexible Molecular Hinge

scientific article published in October 2004

Ribozyme Activity of RNA Nonenzymatically Polymerized from 3′,5′-Cyclic GMP

scientific article published on 3 December 2013

Role of Fine Structural Dynamics in Recognition of Histone H3 by HP1γ(CSD) Dimer and Ability of Force Fields to Describe Their Interaction Network

scientific article published on 18 September 2019

Role of S-turn2 in the Structure, Dynamics, and Function of Mitochondrial Ribosomal A-Site. A Bioinformatics and Molecular Dynamics Simulation Study

scientific article published on 6 June 2014

RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution

scientific article published on 10 September 2019

Selectivity of major isoquinoline alkaloids from Chelidonium majus towards telomeric G-quadruplex: A study using a transition-FRET (t-FRET) assay

scientific article

Sequence dependent intrinsic deformability of the DNA base amino groups. An ab initio quantum chemical analysis

scientific article published in January 1994

Sequential electron transfer governs the UV-induced self-repair of DNA photolesions.

scientific article

Simulations of A-RNA duplexes. The effect of sequence, solute force field, water model, and salt concentration

scientific article published on 9 August 2012

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

scientific article

Spectroscopic and Theoretical Insights into Sequence Effects of Aminofluorene-Induced Conformational Heterogeneity and Nucleotide Excision Repair†,∇

scientific article published in October 2007

Stabilization of the Purine•Purine•Pyrimidine DNA Base Triplets by Divalent Metal Cations

scientific article published in August 1998

Stereocontrolled Synthesis of (-)-Bactobolin A

scientific article published on 14 April 2020

Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations

scientific article published on 28 September 2018

Structural Dynamics of Thrombin-Binding DNA Aptamer d(GGTTGGTGTGGTTGG) Quadruplex DNA Studied by Large-Scale Explicit Solvent Simulations

scientific article

Structural and energetic factors controlling the enantioselectivity of dinucleotide formation under prebiotic conditions

scientific article published in 2013

Structural and evolutionary classification of G/U wobble basepairs in the ribosome

scientific article

Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations

scientific article published on 21 May 2013

Structural interpretation of J coupling constants in guanosine and deoxyguanosine: modeling the effects of sugar pucker, backbone conformation, and base pairing.

scientific article

Structure and dynamics of the ApA, ApC, CpA, and CpC RNA dinucleoside monophosphates resolved with NMR scalar spin-spin couplings.

scientific article published in January 2009

Structure and mechanical properties of the ribosomal L1 stalk three-way junction.

scientific article published on 26 March 2012

Structure of a Stable G-Hairpin.

scientific article published on 20 February 2017

Structure, Energetics, Vibrational Frequencies and Charge Transfer of Base Pairs, Nucleoside Pairs, Nucleotide Pairs and B-DNA Pairs of Trinucleotides:ab initioHF/MINI-1 and Empirical Force Field Study

scientific article published in June 2000

Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer.

scientific article

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations

scientific article published on August 2006

Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation

Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations

scientific article published on October 2005

Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNA.

scientific article published in October 2005

Surprisingly broad applicability of the cc-pVnZ-F12 basis set for ground and excited states

scientific article published on 01 June 2020

Tautomeric equilibrium, stability, and hydrogen bonding in 2'-deoxyguanosine monophosphate complexed with Mg2+.

scientific article published on 11 December 2007

Tetraloop-like geometries could form the basis of the catalytic activity of the most ancient ribooligonucleotides

scientific article published on 29 January 2015

The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies

scientific article published on 16 October 2012

The Effect of Metal Binding to the N7 Site of Purine Nucleotides on Their Structure, Energy, and Involvement in Base Pairing

article published in 2000

The influence of square planar platinum complexes on DNA base pairing. An ab initio DFT study

scientific article published in 2001

The interactions of square platinum(II) complexes with guanine and adenine: a quantum-chemical ab initio study of metalated tautomeric forms.

scientific article published in April 2000

The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.

scientific article

Theoretical Analysis of the Base Stacking in DNA: Choice of the Force Field and a Comparison with the Oligonucleotide Crystal Structures

scientific article published in October 1993

Theoretical calculation of the NMR spin-spin coupling constants and the NMR shifts allow distinguishability between the specific direct and the water-mediated binding of a divalent metal cation to guanine

scientific article

Theoretical studies of the mechanism of 2-aminooxazole formation under prebiotically plausible conditions.

scientific article

Theoretical studies on the intermolecular interactions of potentially primordial base-pair analogues

scientific article published in March 2010

Theoretical study of the guanine --> 6-thioguanine substitution in duplexes, triplexes, and tetraplexes.

scientific article published in November 2004

Theoretical study of the scalar coupling constants across the noncovalent contacts in RNA base pairs: the cis- and trans-watson-crick/sugar edge base pair family

scientific article

Theoretical study on the factors controlling the stability of the borate complexes of ribose, arabinose, lyxose, and xylose

scientific article published in January 2008

Theoretical study on the structure, stability, and electronic properties of the guanine-Zn-cytosine base pair in M-DNA.

scientific article published in February 2007

Thermodynamic characteristics for the formation of H-bonded DNA base pairs

TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth

scientific article

Toward Convergence in Folding Simulations of RNA Tetraloops: Comparison of Enhanced Sampling Techniques and Effects of Force Field Modifications

scientific article published on 01 April 2022

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

scientific article published on May 2013

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

scientific article published in October 2002

Towards biochemically relevant QM computations on nucleic acids: controlled electronic structure geometry optimization of nucleic acid structural motifs using penalty restraint functions.

scientific article published on 27 November 2014

Trans Hoogsteen/sugar edge base pairing in RNA. Structures, energies, and stabilities from quantum chemical calculations

scientific article published in February 2009

Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

article

Two 1 : 1 binding modes for distamycin in the minor groove of d(GGCCAATTGG)

scientific article

UUCG RNA Tetraloop as a Formidable Force-Field Challenge for MD Simulations

scientific article published on 20 November 2020

Ultrafast excited-state dynamics of isocytosine

scientific article published in 2016

Understanding RNA Flexibility Using Explicit Solvent Simulations: The Ribosomal and Group I Intron Reverse Kink-Turn Motifs

scientific article published on 5 August 2011

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

scientific article published in 2012

Untemplated nonenzymatic polymerization of 3',5'cGMP: a plausible route to 3',5'-linked oligonucleotides in primordia

scientific article published on 6 February 2015

Uracil Dimer: Potential Energy and Free Energy Surfaces. Ab Initio beyond Hartree−Fock and Empirical Potential Studies

article published in 1998

W-RESP: Well-Restrained Electrostatic Potential-Derived Charges. Revisiting the Charge Derivation Model

scientific article published on 17 May 2021

Water-chromophore electron transfer determines the photochemistry of cytosine and cytidine.

scientific article

Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics

scientific article published on February 2015

Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER

scientific article published on 28 September 2021

rRNA C-Loops: Mechanical Properties of a Recurrent Structural Motif.

scientific article published on 15 June 2017

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

scientific article

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