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List of works by Michal Otyepka

2,6,8,9-tetrasubstituted purines as new CDK1 inhibitors.

scientific article published in September 2003

2D Chemistry: Chemical Control of Graphene Derivatization

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

scientific article published on 21 August 2012

A cancer-derived mutation in the PSTAIRE helix of cyclin-dependent kinase 2 alters the stability of cyclin binding

scientific article published on 24 April 2010

A computational study of the glycine-rich loop of mitochondrial processing peptidase

scientific article

A high efficiency H2S gas sensor material: paper like Fe2O3/graphene nanosheets and structural alignment dependency of device efficiency

article

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

scientific article published on 5 December 2017

ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece.

scientific article

Accurate surface energies from first principles

scholarly article in Physical Review B, vol. 91 no. 11, March 2015

Activation and inhibition of cyclin-dependent kinase-2 by phosphorylation; a molecular dynamics study reveals the functional importance of the glycine-rich loop

scientific article published on 7 May 2004

Adsorption of Organic Molecules to van der Waals Materials: Comparison of Fluorographene and Fluorographite with Graphene and Graphite.

scientific article

Adsorption of small organic molecules on graphene.

scientific article published on 16 April 2013

Alkynylation of graphene via the Sonogashira C-C cross-coupling reaction on fluorographene

Amphiphilic Drug-Like Molecules Accumulate in a Membrane below the Head Group Region

article by Markéta Paloncýová et al published 21 January 2014 in Journal of Physical Chemistry

Anaerobic Reaction of Nanoscale Zerovalent Iron with Water: Mechanism and Kinetics

Analysis of CDK2 active-site hydration: a method to design new inhibitors

scientific article published in May 2004

Anatomy of enzyme channels

scientific article

Antiallergic effects of pigments isolated from green sea urchin (Strongylocentrotus droebachiensis) shells

scientific article

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

article

Arene C H insertion catalyzed by ferrocene covalently heterogenized on graphene acid

scholarly article in Carbon, vol. 143, March 2019

Assessing the Current State of Amber Force Field Modifications for DNA

scientific article

Band Gaps and Optical Spectra of Chlorographene, Fluorographene and Graphane from G0W0, GW0 and GW Calculations on Top of PBE and HSE06 Orbitals.

scientific article published on 12 August 2013

Band gaps and optical spectra from single- and double-layer fluorographene to graphite fluoride: many-body effects and excitonic states ⬇️

article published in 2014

Band gaps and structural properties of graphene halides and their derivates: A hybrid functional study with localized orbital basis sets ⬇️

scientific article published on July 21, 2012

Band-Edge Engineering at the Carbon Dot–TiO2 Interface by Substitutional Boron Doping

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

scientific article published on August 2014

Behavior of human cytochromes P450 on lipid membranes

scientific article published on 13 September 2013

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

Benchmarking of Force Fields for Molecule-Membrane Interactions

scientific article published on 8 July 2014

Bimodal role of fluorine atoms in fluorographene chemistry opens a simple way toward double functionalization of graphene

scholarly article in Carbon, vol. 145, April 2019

Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site

Biomacromolecular Fragments and Patterns

Biomimetic Superhydrophobic/Superoleophilic Highly Fluorinated Graphene Oxide and ZIF-8 Composites for Oil-Water Separation

article published in 2015

Bonding Motifs in Metal-Organic Compounds on Surfaces

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 Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

scientific article published on 3 February 2015

Carbon-Based Materials at Nanoscale

Challenges in the theoretical description of nanoparticle reactivity: Nano zero-valent iron

scholarly article by František Karlický & Michal Otyepka published 18 February 2014 in International Journal of Quantum Chemistry

Changes in electrostatic surface potential of Na+/K+-ATPase cytoplasmic headpiece induced by cytoplasmic ligand(s) binding.

scientific article published on September 2009

Channel Characteristics

ChannelsDB: database of biomacromolecular tunnels and pores

scientific article published on 3 October 2017

Characterization via Charges

Chemical Tuning of Specific Capacitance in Functionalized Fluorographene

scientific article published on 07 June 2019

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

scientific article published on October 2015

Chemical nature of boron and nitrogen dopant atoms in graphene strongly influences its electronic properties

scholarly article by Petr Lazar et al published 2014 in Physical Chemistry Chemical Physics

Chemistry, properties, and applications of fluorographene

Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals.

scientific article published on March 2015

Coarse-grain simulations of skin ceramide NS with newly derived parameters clarify structure of melted phase

scientific article published on 25 February 2015

Combined high degree of carboxylation and electronic conduction in graphene acid sets new limits for metal free catalysis in alcohol oxidation

scientific article published on 06 September 2019

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

scientific article published on April 2014

Complete Process of Data Extraction and Analysis

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

Concluding Remarks

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

Convergence of Free Energy Profile of Coumarin in Lipid Bilayer ⬇️

scientific article published on February 24, 2012

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

Correlation of Dissociation Constants of 2- and 2,6-Substituted Anilines in Water by Methods Based on the Similarity Principle and Quantum-Chemistry Calculations

Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues

scientific article

Cyanographene and Graphene Acid: Emerging Derivatives Enabling High-Yield and Selective Functionalization of Graphene

scientific article published on 16 February 2017

Cyanographene and Graphene Acid: The Functional Group of Graphene Derivative Determines the Application in Electrochemical Sensing and Capacitors

Density-functional, density-functional tight-binding, and wave function calculations on biomolecular systems.

scientific article published on 06 April 2007

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

Detection and Extraction of Fragments

Detection of Channels

Dichlorocarbene-Functionalized Fluorographene: Synthesis and Reaction Mechanism

scientific article published on 4 May 2015

Different mechanisms of CDK5 and CDK2 activation as revealed by CDK5/p25 and CDK2/cyclin A dynamics

scientific article published on 9 January 2006

Dimerization of quercetin, Diels-Alder vs. radical-coupling approach: a joint thermodynamics, kinetics, and topological study.

scientific article

Direct mapping of chemical oxidation of individual graphene sheets through dynamic force measurements at the nanoscale

scientific article published on 13 October 2016

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

scientific article

Dissociation of Water at Iron Surfaces: Generalized Gradient Functional and Range-Separated Hybrid Functional Study

Docking-Based Development of Purine-like Inhibitors of Cyclin-Dependent Kinase-2

article

Doping with Graphitic Nitrogen Triggers Ferromagnetism in Graphene

scientific article published on 23 January 2017

Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations

article

Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations

scientific article published in October 2002

Editorial: cytochromes P450: flexibility and plasticity - properties determining substrate preferences

scientific article

Effect of Cholesterol on the Structure of Membrane-Attached Cytochrome P450 3A4

article published in 2015

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

article

Effect of Lipid Charge on Membrane Immersion of Cytochrome P450 3A4.

scientific article

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

scientific article published on 28 June 2017

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

Environmental Applications of Chemically Pure Natural Ferrihydrite

scientific article published on 01 June 2007

Exact roles of individual chemical forms of nitrogen in the photoluminescent properties of nitrogen-doped carbon dots

Exercises Solution

Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact

article

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

scientific article

Exponential repulsion improves structural predictability of molecular docking

scientific article published on 13 September 2016

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme

scientific article published on May 2010

Ferromagnetism: Sulfur Doping Induces Strong Ferromagnetic Ordering in Graphene: Effect of Concentration and Substitution Mechanism (Adv. Mater. 25/2016).

scientific article published in July 2016

First Step in the Reaction of Zerovalent Iron with Water

scientific article published on 9 August 2011

First-principles study of the mechanism of wettability transition of defective graphene

scientific article

Flexibility of human cytochrome P450 enzymes: molecular dynamics and spectroscopy reveal important function-related variations

scientific article published on 23 July 2010

Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences

scientific article

Flow induced HeLa cell detachment kinetics show that oxygen-containing functional groups in graphene oxide are potent cell adhesion enhancers

scientific article published on 01 February 2019

Fluorinated graphenes as advanced biosensors - effect of fluorine coverage on electron transfer properties and adsorption of biomolecules

scientific article published in June 2016

Fluorographites (CF(x))n exhibit improved heterogeneous electron-transfer rates with increasing level of fluorination: towards the sensing of biomolecules

scientific article published on 11 April 2014

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

scientific article

Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign

scientific article published on April 2012

Functional Nanosheet Synthons by Covalent Modification of Transition-Metal Dichalcogenides

Functional flexibility of human cyclin-dependent kinase-2 and its evolutionary conservation

scientific article

Functionalization of Graphene: Covalent and Non-Covalent Approaches, Derivatives and Applications

scientific article published on 14 November 2012

Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domains

scientific article published on May 2002

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility

scientific article published on 8 August 2008

Glycine-rich loop of mitochondrial processing peptidase alpha-subunit is responsible for substrate recognition by a mechanism analogous to mitochondrial receptor Tom20.

scientific article published on 4 January 2010

Graphene fluoride: a stable stoichiometric graphene derivative and its chemical conversion to graphene

scientific article

Graphitic Nitrogen Doping in Carbon Dots Causes Red-Shifted Absorption

article by Sunandan Sarkar et al published 6 January 2016 in Journal of Physical Chemistry C

Graphitic Nitrogen Triggers Red Fluorescence in Carbon Dots.

scientific article published on 14 November 2017

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

scientific article published on 3 October 2015

Halogenated graphenes: rapidly growing family of graphene derivatives

scientific article published on 15 July 2013

High-Performance Supercapacitors Based on a Zwitterionic Network of Covalently Functionalized Graphene with Iron Tetraaminophthalocyanine

High-Yield Alkylation and Arylation of Graphene via Grignard Reaction with Fluorographene.

scientific article published on 29 January 2017

How the Stabilization of INK4 Tumor Suppressor 3D Structure Evaluated by Quantum Chemical and Molecular Mechanics Calculations Corresponds Well with Experimental Results: Interplay of Association Enthalpy, Entropy, and Solvation Effects

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

Hydrophilic Nanotube Supported Graphene-Water Dispersible Carbon Superstructure with Excellent Conductivity

IMPROVING THE PERFORMANCE OF THE RNA AMBER FORCE FIELD BY TUNING THE HYDROGEN-BONDING INTERACTIONS

Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles

scientific article published in January 2007

Immobilized Enzymes on Graphene as Nanobiocatalyst

scientific article published on 30 December 2019

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

scientific article published on 02 April 2019

In silico pharmacology: Drug membrane partitioning and crossing

scientific article

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

Insenstivity to Close Contacts and Inability to Predict Protein Foldability ⬇️

scientific article published on February 1, 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 for the purine inhibitor roscovitine with cyclin-dependent kinase 2: correlated ab initio quantum-chemical, DFT and empirical calculations

scientific article published on May 2006

Interaction of Graphene and Arenes with Noble Metals

article

Interaction of single- and double-stranded DNA with multilayer MXene by fluorescence spectroscopy and molecular dynamics simulations

scientific article published on 23 September 2019

Interaction of the Helium, Hydrogen, Air, Argon, and Nitrogen Bubbles with Graphite Surface in Water

scientific article published on 5 May 2017

Interplay between Ethanol Adsorption to High-Energy Sites and Clustering on Graphene and Graphite Alters the Measured Isosteric Adsorption Enthalpies

Introduction

Is Single Layer MoS2 Stable in the Air?

scientific article

Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450?

scientific article published on February 2012

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

Ligand effects on single-electron transfer of isolated iron atoms in the gaseous complexes [(OC)mFe(OH2)n]+ (m, n=0–2, m+n=1, 2)

Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant

article published in 2013

Lipid Enhanced Exfoliation for Production of Graphene Nanosheets

article

Lipocarbazole, an efficient lipid peroxidation inhibitor anchored in the membrane

scholarly article by Gabin Fabre published in August 2015

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

scientific article (publication date: 16 August 2013)

MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels

scientific article published in November 2007

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels

scientific article

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).

scientific article published in July 2018

Malonate-based inhibitors of mammalian serine racemase: kinetic characterization and structure-based computational study.

scientific article published on 16 October 2014

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

scientific article published on 8 November 2017

Mechanism of enhanced conversion of 1,2,3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling.

scientific article

Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site

scientific article

Membrane-attached mammalian cytochromes P450: An overview of the membrane's effects on structure, drug binding, and interactions with redox partners

scientific article published on 5 March 2018

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

Modelling of graphene functionalization

scientific article published in September 2015

Mole 2.5 - Tool for Detection and Analysis of Macromolecular Pores and Channels

scholarly article by Karel Berka et al published February 2017 in Biophysical Journal

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

article

Molecular Insight into Affinities of Drugs and Their Metabolites to Lipid Bilayers ⬇️

scientific article published on February 19, 2013

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 insights into the role of a distal F240A mutation that alters CYP1A1 activity towards persistent organic pollutants.

scientific article published on 2 August 2017

Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study

scientific article published on 12 October 2012

Morphology-Dependent Magnetism in Nanographene: Beyond Nanoribbons

Multidrug resistance-associated protein 4 (MRP4) controls ganciclovir intracellular accumulation and contributes to ganciclovir-induced neutropenia in renal transplant patients

scientific article

NZVI modified magnetic filter paper with high redox and catalytic activities for advanced water treatment technologies

article

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

scientific article published in June 2013

Nature of Absorption Bands in Oxygen-Functionalized Graphitic Carbon Dots

Non-covalent control of spin-state in metal-organic complex by positioning on N-doped graphene

scientific article published in Nature Communications

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

Noncovalent Integration of a Bioinspired Ni Catalyst to Graphene Acid for Reversible Electrocatalytic Hydrogen Oxidation

scientific article published on 22 January 2020

Nonenzymatic Oligomerization of 3',5'-Cyclic CMP Induced by Proton and UV Irradiation Hints at a Nonfastidious Origin of RNA.

scientific article published on 4 May 2017

On the Possible Effect of Phytic Acid (Myo-Inositol Hexaphosphoric Acid, IP6) on Cytochromes P450 and Systems of Xenobiotic Metabolism in Different Hepatic Models

scientific article published in 2024

One-Step Synthesis of Janus Fluorographene Derivatives

scientific article published on 06 February 2020

Optical properties of wine pigments: theoretical guidelines with new methodological perspectives

scientific article published in May 2015

Organic adsorbates have higher affinities to fluorographene than to graphene

article

Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes

scientific article published on 01 August 2019

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

Photoluminescence effects of graphitic core size and surface functional groups in carbon dots: COO− induced red-shift emission

article by Katerina Hola et al published April 2014 in Carbon

Photoluminescent Carbon Nanostructures

Positioning of Antioxidant Quercetin and Its Metabolites in Lipid Bilayer Membranes: Implication for Their Lipid-Peroxidation Inhibition

Positive and Negative Effects of Dopants toward Electrocatalytic Activity of MoS2 and WS2: Experiments and Theory

scientific article published on 23 April 2020

Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics

scientific article published on July 2010

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

scientific article published on 8 November 2011

Quantification of the Interaction Forces between Metals and Graphene by Quantum Chemical Calculations and Dynamic Force Measurements under Ambient Conditions

article

Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy

scientific article published on 6 September 2013

Quantum Monte Carlo for noncovalent interactions: an efficient protocol attaining benchmark accuracy ⬇️

scientific article published on 29 August 2014

Quaternized carbon dot-modified graphene oxide for selective cell labelling--controlled nucleus and cytoplasm imaging.

scientific article published on September 2014

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

scientific article published on 3 January 2018

RNA nanopatterning on graphene

Random Phase Approximation in Surface Chemistry: Water Splitting on Iron

scientific article published on 25 July 2013

Rationalization of reduced penetration of drugs through ceramide gel phase membrane

scientific article

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

Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives

scientific article published on 2 April 2015

Reactivity of fluorographene is triggered by point defects: beyond the perfect 2D world.

scientific article published on 14 February 2018

Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

scientific article

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

scientific article

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

scientific article published on 02 August 2011

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

Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations

scientific article published on 10 May 2008

Role of Enzyme Flexibility in Ligand Access and Egress to Active Site: Bias-Exchange Metadynamics Study of 1,3,7-Trimethyluric Acid in Cytochrome P450 3A4.

scientific article published on 11 March 2016

Role of the Edge Properties in the Hydrogen Evolution Reaction on MoS2.

scientific article published on 18 January 2017

Role of the puckered anisotropic surface in the surface and adsorption properties of black phosphorus

scientific article

Room temperature organic magnets derived from sp3 functionalized graphene

scientific article published on 20 February 2017

Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods

scientific article published in February 2008

Selective Functionalization Blended with Scaffold Conductivity in Graphene Acid Promotes H2O2 Electrochemical Sensing

scientific article published on 15 November 2019

Semiempirical Quantum Mechanical Method PM6-DH2X Describes the Geometry and Energetics of CK2-Inhibitor Complexes Involving Halogen Bonds Well, While the Empirical Potential Fails

scientific article published on 16 June 2011

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

scientific article published on 9 August 2012

Spin-Crossing in an Organometallic Pt-Benzene Complex

scientific article published on 28 February 2013

Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment

scientific article published on 9 March 2016

Structural Bioinformatics Databases of General Use

Structural Bioinformatics Tools for Drug Design

Structural Changes in Ceramide Bilayers Rationalize Increased Permeation through Stratum Corneum Models with Shorter Acyl Tails

scientific article

Structural Dynamics of Carbon Dots in Water and N, N-Dimethylformamide Probed by All-Atom Molecular Dynamics Simulations.

scientific article published on 9 March 2018

Structural dynamics of propeller loop: towards folding of RNA G-quadruplex

Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms

scientific article published on 10 March 2018

Structural properties of CYP2D6: requirements for substrates and inhibitors

Structure, dynamical stability, and electronic properties of phases inTaS2from a high-level quantum mechanical calculation

scientific article published on 8 December 2015

Sulfur Doping Induces Strong Ferromagnetic Ordering in Graphene: Effect of Concentration and Substitution Mechanism.

scientific article published on 2 May 2016

Surface energy analysis (SEA) and rheology of powder milk dairy products

scientific article published on 08 November 2014

Surface energy analysis (SEA) study of hyaluronan powders

Surface heterogeneity: Information from inverse gas chromatography and application to model pharmaceutical substances

article

Surface properties of MoS2 probed by inverse gas chromatography and their impact on electrocatalytic properties

scientific article published on 30 November 2017

Surface termination of MgB2 unveiled by a combination of adsorption experiments and theoretical calculations

scientific article published on 01 April 2019

Synergism of antioxidant action of vitamins E, C and quercetin is related to formation of molecular associations in biomembranes

Tailoring π-conjugation and vibrational modes to steer on-surface synthesis of pentalene-bridged ladder polymers

scientific article published on 11 September 2020

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 Nature of the Binding of Au, Ag, and Pd to Benzene, Coronene, and Graphene: From Benchmark CCSD(T) Calculations to Plane-Wave DFT Calculations

scientific article

The Role of Protein-Protein and Protein-Membrane Interactions on P450 Function

scientific article (publication date: April 2016)

The mechanism of inhibition of the cyclin-dependent kinase-2 as revealed by the molecular dynamics study on the complex CDK2 with the peptide substrate HHASPRK

scientific article

The nature of bonding and electronic properties of graphene and benzene with iridium adatoms

scientific article published on 28 August 2014

The nature of high surface energy sites in graphene and graphite

scholarly article in Carbon, vol. 73, July 2014

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

scientific article

The surface and structural properties of graphite fluoride

scholarly article in Carbon, vol. 94, November 2015

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

scientific article published on 04 May 2009

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

scientific article published in March 2010

Thermally reduced fluorographenes as efficient electrode materials for supercapacitors

scientific article published on 01 November 2019

Thiofluorographene-Hydrophilic Graphene Derivative with Semiconducting and Genosensing Properties

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

Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors.

scientific article published in February 2011

Tunable one-step double functionalization of graphene based on fluorographene chemistry

scientific article published on 01 February 2020

Tuning the UV spectrum of PAHs by means of different N-doping types taking pyrene as paradigmatic example: categorization via valence bond theory and high-level computational approaches

scientific article published on 25 September 2020

Tuning the magnetic properties of graphene derivatives by functional group selection

scientific article published on 03 June 2019

Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c

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

scientific article published on 20 November 2020

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

scientific article published on 5 August 2011

Validation

book chapter in Structural Bioinformatics Tools for Drug Design (2016)

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

scientific article published on 17 May 2021

Water dispersible functionalized graphene fluoride with significant nonlinear optical response

article

What common structural features and variations of mammalian P450s are known to date?

scientific article published on 29 September 2006

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

scientific article published on February 2015

Zigzag sp2 Carbon Chains Passing through an sp3 Framework: A Driving Force toward Room-Temperature Ferromagnetic Graphene

scientific article published on 10 December 2018

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