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(2963) Proposal to reject the name <i>Rubus pseudoidaeus</i> (<i>Rosaceae</i>)

artículo científico publicado en 2023

A QM/MM investigation of the activation and catalytic mechanism of Fe-only hydrogenases

artículo científico publicado en 2007

A QM/MM study of the binding of RAPTA ligands to cathepsin B

artículo científico publicado en 2011

A combined computational and experimental investigation of the [2Fe-2S] cluster in biotin synthase.

artículo científico publicado en 2009

A comparison of different initialization protocols to obtain statistically independent molecular dynamics simulations ⬇️

artículo científico publicado el 30 de enero de 2011

A five-coordinate [2Fe-2S] cluster.

artículo científico publicado en 2010

A large-scale test of free-energy simulation estimates of protein-ligand binding affinities.

artículo científico publicado en 2014

A novel mechanism of heme degradation to biliverdin studied by QM/MM and QM calculations

artículo científico publicado en 2018

A quantum-mechanical study of the reaction mechanism of sulfite oxidase

scientific article published on 24 June 2014

A semiempirical approach to ligand-binding affinities: dependence on the Hamiltonian and corrections

artículo científico publicado en 2012

A synthetic analogue of Rieske-type [2Fe-2S] clusters

scientific article published on 01 January 2008

Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models

artículo científico publicado en 2007

Accuracy of typical approximations in classical models of intermolecular polarization

scientific article published on 01 January 2008

Accurate QM/MM Free Energy Calculations of Enzyme Reactions:  Methylation by Catechol O-Methyltransferase

artículo científico publicado en 2005

Accurate Reaction Energies in Proteins Obtained by Combining QM/MM and Large QM Calculations

artículo científico publicado en 2012

Accurate calculations of geometries and singlet–triplet energy differences for active-site models of [NiFe] hydrogenase

artículo científico publicado en 2014

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration

artículo científico publicado en 2011

Amino acid oxidation of Candida antarctica lipase B studied by molecular dynamics simulations and site-directed mutagenesis.

artículo científico publicado en 2013

An MM/3D-RISM approach for ligand binding affinities.

artículo científico publicado en 2010

An automatic method to generate force-field parameters for hetero-compounds.

artículo científico publicado en 2003

An improved method to predict the entropy term with the MM/PBSA approach.

artículo científico publicado en 2008

Are crystallographic B-factors suitable for calculating protein conformational entropy?

artículo científico publicado en 2019

Assessing the stability of free-energy perturbation calculations by performing variations in the method.

artículo científico publicado en 2018

Benchmark Study of Redox Potential Calculations for Iron–Sulfur Clusters in Proteins

artículo científico publicado en 2022

Binding affinities by alchemical perturbation using QM/MM with a large QM system and polarizable MM model

artículo científico publicado en 2015

Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods

article

Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA.

artículo científico publicado en 2011

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.

artículo científico publicado en 2017

Binding free energies in the SAMPL5 octa-acid host-guest challenge calculated with DFT-D3 and CCSD(T).

scientific article published on 06 September 2016

Binding free energies in the SAMPL6 octa-acid host-guest challenge calculated with MM and QM methods

scientific article published on 10 September 2018

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

artículo científico publicado en 2016

Calculation of protein-ligand interaction energies by a fragmentation approach combining high-level quantum chemistry with classical many-body effects

scientific article published on 01 August 2009

Can MM/GBSA calculations be sped up by system truncation?

artículo científico publicado en 2017

Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?

artículo científico publicado en 2017

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods

artículo científico publicado en 2015

Combined quantum and molecular mechanics calculations on metalloproteins.

artículo científico publicado en 2003

Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations ⬇️

artículo científico publicado el 18 de abril de 2013

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

scientific article published on 20 July 2011

Comparison of QM/MM Methods To Obtain Ligand-Binding Free Energies.

artículo científico publicado en 2017

Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies

artículo científico publicado en 2012

Comparison of overlap-based models for approximating the exchange-repulsion energy

artículo científico publicado en 2006

Comparison of the Chemical Properties of Iron and Cobalt Porphyrins and Corrins ⬇️

artículo científico publicado el 9 de mayo de 2003

Comparison of the Efficiency of the LIE and MM/GBSA Methods to Calculate Ligand-Binding Energies

scientific article published on 19 October 2011

Comparison of the active-site design of molybdenum oxo-transfer enzymes by quantum mechanical calculations

artículo científico publicado en 2014

Computational modelling of oxygenation processes in enzymes and biomimetic model complexes

artículo científico publicado en 2013

Conformational Dependence of Isotropic Polarizabilities

artículo científico publicado en 2011

Conformational Entropies and Order Parameters: Convergence, Reproducibility, and Transferability

scientific article published on 01 January 2014

Conformational dependence of charges in protein simulations.

artículo científico publicado en 2009

Conformational entropy changes upon lactose binding to the carbohydrate recognition domain of galectin-3.

artículo científico publicado en 2009

Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations

artículo científico publicado en 2012

Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

scientific article published on 27 April 2016

Conversion of Homocysteine to Methionine by Methionine Synthase: A Density Functional Study ⬇️

artículo científico publicado el 19 de noviembre de 2003

Coupled-cluster interaction energies for 200-atom host-guest systems

artículo científico publicado en 2014

Do quantum mechanical energies calculated for small models of protein-active sites converge?

artículo científico publicado en 2009

Does DFT-D estimate accurate energies for the binding of ligands to metal complexes?

artículo científico publicado en 2011

Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems?

artículo científico publicado en 2016

Dynamics of Water Molecules in the Active-Site Cavity of Human Cytochromes P450

article

Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins

artículo científico publicado en 2013

Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.

artículo científico publicado en 2014

Estimates of ligand-binding affinities supported by quantum mechanical methods.

artículo científico publicado en 2010

Exploration of H2 binding to the [NiFe]-hydrogenase active site with multiconfigurational density functional theory.

artículo científico publicado en 2017

Exploring ligand dynamics in protein crystal structures with ensemble refinement

artículo científico publicado en 2021

Extremely large differences in DFT energies for nitrogenase models

scientific article published on 01 January 2019

Free-energy perturbation and quantum mechanical study of SAMPL4 octa-acid host-guest binding energies

artículo científico publicado en 2014

Functionally relevant interplay between the Fe(4)S(4) cluster and CN(-) ligands in the active site of [FeFe]-hydrogenases.

artículo científico publicado en 2010

General Transition-State Force Field for Cytochrome P450 Hydroxylation

artículo científico publicado en 2007

Geometry and Electronic Structure of the P-Cluster in Nitrogenase Studied by Combined Quantum Mechanical and Molecular Mechanical Calculations and Quantum Refinement

artículo científico publicado en 2019

H2 binding to the active site of [NiFe] hydrogenase studied by multiconfigurational and coupled-cluster methods

artículo científico publicado en 2017

Higher Flexibility of Glu-172 Explains the Unusual Stereospecificity of Glyoxalase I

artículo científico publicado en 2018

Host-Guest Relative Binding Affinities at Density-Functional Theory Level from Semiempirical Molecular Dynamics Simulations

scientific article published on 13 March 2019

How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging

artículo científico publicado en 2017

How accurate are continuum solvation models for drug-like molecules?

artículo científico publicado en 2009

How accurate can a force field become? A polarizable multipole model combined with fragment-wise quantum-mechanical calculations

scientific article published on 01 January 2009

How to obtain statistically converged MM/GBSA results.

artículo científico publicado en 2010

Hybrids between Rubus caesius and Rubus sect. Corylifolii (Rosaceae) and their relation to R. cyclomorphus , R. tiliaster , R. glauciformis , R. slesvicensis and R. firmus ⬇️

artículo científico publicado en 2022

Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements

artículo científico publicado en 2007

Implicit versus explicit solvent in free energy calculations of enzyme catalysis: Methyl transfer catalyzed by catechol O-methyltransferase

artículo científico publicado en 2006

Improving the Efficiency of Protein-Ligand Binding Free-Energy Calculations by System Truncation

artículo científico publicado en 2012

Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding

scientific article published on 23 January 2019

Is density functional theory accurate for lytic polysaccharide monooxygenase enzymes?

artículo científico publicado en 2020

Isocyanide in biochemistry? A theoretical investigation of the electronic effects and energetics of cyanide ligand protonation in [FeFe]-hydrogenases

scientific article published on 12 January 2011

Large Density-Functional and Basis-Set Effects for the DMSO Reductase Catalyzed Oxo-Transfer Reaction.

artículo científico publicado en 2013

Large equatorial ligand effects on C-H bond activation by nonheme iron(IV)-oxo complexes

artículo científico publicado en 2014

Ligand Affinities Estimated by Quantum Chemical Calculations

artículo científico publicado en 2010

Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.

artículo científico publicado en 2006

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.

artículo científico publicado en 2016

Mechanism of hydrogen peroxide formation by lytic polysaccharide monooxygenase.

artículo científico publicado en 2018

Mechanistic and Physiological Implications of the Interplay among Iron–Sulfur Clusters in [FeFe]-Hydrogenases. A QM/MM Perspective ⬇️

artículo científico publicado el 26 de octubre de 2011

Metal binding to Bacillus subtilis ferrochelatase and interaction between metal sites

artículo científico publicado en 2003

Molecular mechanism of lytic polysaccharide monooxygenases.

artículo científico publicado en 2018

Multireference Ab Initio Calculations on Reaction Intermediates of the Multicopper Oxidases

artículo científico publicado en 2006

Multiscale Modelling of Lytic Polysaccharide Monooxygenases

artículo científico publicado en 2017

Multiscale modeling of the active site of [Fe] hydrogenase: the H₂ binding site in open and closed protein conformations

artículo científico publicado en 2015

NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S.

artículo científico publicado en 2005

Neutron structures of <i>Leishmania mexicana</i> triosephosphate isomerase in complex with reaction-intermediate mimics shed light on the proton-shuttling steps

artículo científico publicado en 2021

Nonpolar Solvation Free Energies of Protein-Ligand Complexes

scientific article published on 28 September 2010

O2 Activation in Salicylate 1,2-Dioxygenase: A QM/MM Study Reveals the Role of His162.

artículo científico publicado en 2016

O2-binding to heme: electronic structure and spectrum of oxyheme, studied by multiconfigurational methods

artículo científico publicado en 2005

On the Convergence of QM/MM Energies

scientific article published on 07 February 2011

On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies

scientific article published on 13 July 2021

On the role of the axial ligand in heme proteins: a theoretical study.

artículo científico publicado en 2004

On the significance of hydrogen bonds for the discrimination between CO and O2 by myoglobin

scientific article published on 01 February 1999

Performance of density functionals for first row transition metal systems

scientific article published on 01 January 2007

Predicting Relative Binding Affinity Using Nonequilibrium QM/MM Simulations

artículo científico publicado en 2018

Prediction of activation energies for aromatic oxidation by cytochrome P450.

artículo científico publicado en 2008

Probing the effects of one-electron reduction and protonation on the electronic properties of the Fe-S clusters in the active-ready form of [FeFe]-hydrogenases. A QM/MM investigation

scientific article published on 14 November 2011

Protein Influence on Electronic Spectra Modeled by Multipoles and Polarizabilities

artículo científico publicado en 2009

Proton Transfer at Metal Sites in Proteins Studied by Quantum Mechanical Free-Energy Perturbations

artículo científico publicado en 2008

Protonation States of Homocitrate and Nearby Residues in Nitrogenase Studied by Computational Methods and Quantum Refinement

artículo científico publicado en 2017

Protonation and reduction of the FeMo cluster in nitrogenase studied by QM/MM calculations

article

Protonation states of intermediates in the reaction mechanism of [NiFe] hydrogenase studied by computational methods

artículo científico publicado en 2016

QM/MM Calculations on Proteins.

artículo científico publicado en 2016

QM/MM Study of the Catalytic Reaction of Myrosinase; Importance of Assigning Proper Protonation States of Active-Site Residues

artículo científico publicado en 2021

QM/MM Study of the Conversion of Oxophlorin into Verdoheme by Heme Oxygenase.

artículo científico publicado en 2017

QM/MM study of the insertion of metal ion into protoporphyrin IX by ferrochelatase

artículo científico publicado en 2009

QM/MM study of the reaction mechanism of sulfite oxidase.

artículo científico publicado en 2018

QM/MM-PBSA method to estimate free energies for reactions in proteins.

artículo científico publicado en 2008

Quantum Mechanics/Molecular Mechanics Study of the Reaction Mechanism of Glyoxalase I

artículo científico publicado en 2020

Quantum Refinement Does Not Support Dinuclear Copper Sites in Crystal Structures of Particulate Methane Monooxygenase

artículo científico publicado en 2017

Quantum chemistry can locally improve protein crystal structures.

artículo científico publicado en 2003

Quantum mechanical free energy barrier for an enzymatic reaction

artículo científico publicado en 2005

Quantum refinement of [FeFe] hydrogenase indicates a dithiomethylamine ligand.

artículo científico publicado en 2010

Reaction Mechanism of [NiFe] Hydrogenase Studied by Computational Methods

artículo científico publicado en 2018

Reaction mechanism of manganese superoxide dismutase studied by combined quantum and molecular mechanical calculations and multiconfigurational methods.

artículo científico publicado en 2009

Reaction mechanism of porphyrin metallation studied by theoretical methods.

artículo científico publicado en 2005

Redesign of the coenzyme specificity in L-lactate dehydrogenase from bacillus stearothermophilus using site-directed mutagenesis and media engineering

scientific article published on 01 October 1999

Reduction potentials and acidity constants of Mn superoxide dismutase calculated by QM/MM free-energy methods.

artículo científico publicado en 2011

Reductive cleavage of the O-O bond in multicopper oxidases: a QM/MM and QM study

artículo científico publicado en 2011

Relative Ligand-Binding Free Energies Calculated from Multiple Short QM/MM MD Simulations

scientific article published on 25 May 2018

Reorganization energy for internal electron transfer in multicopper oxidases

artículo científico publicado en 2011

Restrained point-charge models for disaccharides.

artículo científico publicado en 2002

Secondary bonding interactions in biomimetic [2Fe-2S] clusters.

artículo científico publicado en 2008

Simulation of the isotropic EXAFS spectra for the S2 and S3 structures of the oxygen evolving complex in photosystem II.

artículo científico publicado en 2015

Starting-Condition Dependence of Order Parameters Derived from Molecular Dynamics Simulations.

artículo científico publicado en 2010

Structural and photoluminescence properties of excited state intramolecular proton transfer capable compounds-potential emissive and electron transport materials

artículo científico publicado en 2006

Structural insights into the active-ready form of [FeFe]-hydrogenase and mechanistic details of its inhibition by carbon monoxide

artículo científico publicado en 2007

Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight into Solvation Effects and Multipolar Interactions

artículo científico publicado en 2019

Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach

artículo científico publicado en 2006

Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases.

artículo científico publicado en 2006

Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects

scientific article published on 01 January 2019

Sulfoxide, Sulfur, and Nitrogen Oxidation and Dealkylation by Cytochrome P450

scientific article published on 01 August 2008

Targeting intermediates of [FeFe]-hydrogenase by CO and CN vibrational signatures.

artículo científico publicado en 2011

The Carbohydrate-Binding Site in Galectin-3 Is Preorganized To Recognize a Sugarlike Framework of Oxygens: Ultra-High-Resolution Structures and Water Dynamics

artículo científico publicado en 2012

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

artículo científico publicado en 2015

The coordination of the catalytic zinc in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations

artículo científico publicado en 1996

The cupric geometry of blue copper proteins is not strained.

artículo científico publicado en 1996

The influence of axial ligands on the reduction potential of blue copper proteins.

artículo científico publicado en 1999

The neutron structure of urate oxidase resolves a long-standing mechanistic conundrum and reveals unexpected changes in protonation

artículo científico publicado en 2014

The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant

scientific article published on 02 August 2012

The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement.

artículo científico publicado en 2004

The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations

artículo científico publicado en 2006

The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron.

artículo científico publicado en 2006

Theoretical 57Fe Mössbauer spectroscopy: isomer shifts of [Fe]-hydrogenase intermediates

artículo científico publicado en 2014

Transition-State Docking of Flunitrazepam and Progesterone in Cytochrome P450.

artículo científico publicado en 2008

Two-Substrate Glyoxalase I Mechanism: A Quantum Mechanics/Molecular Mechanics Study

artículo científico publicado en 2020

Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins.

artículo científico publicado en 2013

Unraveling the Reaction Mechanism of Mo/Cu CO Dehydrogenase Using QM/MM Calculations

artículo científico publicado en 2022

Unraveling the similarity of the photoabsorption of deprotonated p-coumaric acid in the gas phase and within the photoactive yellow protein.

artículo científico publicado en 2010

What Is the Structure of the E4 Intermediate in Nitrogenase?

artículo científico publicado en 2020

Which functional groups of the molybdopterin ligand should be considered when modeling the active sites of the molybdenum and tungsten cofactors? A density functional theory study.

artículo científico publicado en 2009

Why does sulfite reductase employ siroheme?

artículo científico publicado en 2019

Will molecular dynamics simulations of proteins ever reach equilibrium? ⬇️

artículo científico publicado el 22 de mayo de 2012

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