(Q29041457)

27 March 2017

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R. Thomas Ullmann

1

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27 March 2017

G. Matthias Ullmann

series ordinal

2

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27 March 2017

publication date

25 January 2012

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Journal of Computational Chemistry

27 March 2017

published in

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27 March 2017

volume

33

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27 March 2017

issue

8

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27 March 2017

page(s)

887-900

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Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis

27 March 2017

cites work

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pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model

21 January 2018

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Multiple-site titration curves of proteins: an analysis of exact and approximate methods for their calculation

21 January 2018

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Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides

21 January 2018

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Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility

21 January 2018

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Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties

21 January 2018

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Electrostatic models for computing protonation and redox equilibria in proteins.

21 January 2018

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Model for proton transport coupled to protein conformational change: application to proton pumping in the bacteriorhodopsin photocycle.

21 January 2018

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Investigating the mechanisms of photosynthetic proteins using continuum electrostatics

21 January 2018

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Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations.

21 January 2018

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Macroscopic electrostatic models for protonation states in proteins

21 January 2018

1 reference

Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.

21 January 2018

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Multiple protonation equilibria in electrostatics of protein-protein binding

21 January 2018

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Combining conformational flexibility and continuum electrostatics for calculating pK(a)s in proteins

21 January 2018

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Optimizing pKa computation in proteins with pH adapted conformations.

21 January 2018

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Histidine in continuum electrostatics protonation state calculations

21 January 2018

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A generalized free energy perturbation theory accounting for end states with differing configuration space volume.

21 January 2018

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Equilibrium free-energy differences from nonequilibrium measurements: A master-equation approach

21 January 2018

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The influence of a transmembrane pH gradient on protonation probabilities of bacteriorhodopsin: the structural basis of the back-pressure effect

21 January 2018

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Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatic calculations into the regulation of proton pumping.

21 January 2018

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Influence of the membrane potential on the free energy of an intrinsic protein

21 January 2018

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Theory of free energy and entropy in noncovalent binding

21 January 2018

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Calculations of enzymatic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes.

21 January 2018

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Quality of random number generators significantly affects results of Monte Carlo simulations for organic and biological systems

21 January 2018

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Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator

21 January 2018

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A Novel View of pH Titration in Biomolecules†

21 January 2018

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VMD: visual molecular dynamics

21 January 2018

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Equation of State Calculations by Fast Computing Machines

21 January 2018

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Electrostatic calculations of amino acid titration and electron transfer, Q-AQB-->QAQ-B, in the reaction center

21 January 2018

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Calculated coupling of electron and proton transfer in the photosynthetic reaction center of Rhodopseudomonas viridis

21 January 2018

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Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis.

21 January 2018

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The coupling of electron transfer and proton translocation: electrostatic calculations on Paracoccus denitrificans cytochrome c oxidase

21 January 2018

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pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states

21 January 2018

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Calculating pKa values in enzyme active sites

21 January 2018

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Effects of histidine protonation and phosphorylation on histidine-containing phosphocarrier protein structure, dynamics, and physicochemical properties.

21 January 2018

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Mechanistic insights into ferredoxin-NADP(H) reductase catalysis involving the conserved glutamate in the active site

21 January 2018

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Distinguishing two groups of flavin reductases by analyzing the protonation state of an active site carboxylic acid.

21 January 2018

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Cysteine as a modulator residue in the active site of xenobiotic reductase A: a structural, thermodynamic and kinetic study

21 January 2018

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Structural basis for a Kolbe-type decarboxylation catalyzed by a glycyl radical enzyme

21 January 2018

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Determination of electrostatic interaction energies and protonation state populations in enzyme active sites.

21 January 2018

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Remeasuring HEWL pK(a) values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pK(a) calculations

21 January 2018

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pH-Dependent pKaValues in Proteins—A Theoretical Analysis of Protonation Energies with Practical Consequences for Enzymatic Reactions

21 January 2018

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Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c3 using continuum electrostatics.

21 January 2018

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Analysis of the electrochemistry of hemes with E(m)s spanning 800 mV.

21 January 2018

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Efficient, Multiple-Range Random Walk Algorithm to Calculate the Density of States

21 January 2018

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Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram

21 January 2018

1 reference

Good practices in free-energy calculations

21 January 2018

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Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method.

21 January 2018

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Efficiency of alchemical free energy simulations. II. Improvements for thermodynamic integration.

21 January 2018

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Solvation free energies of amino acid side chain analogs for common molecular mechanics water models.

21 January 2018

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Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

21 January 2018

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Double-mutant cycles: a powerful tool for analyzing protein structure and function

21 January 2018

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Density functional calculation of p K(a) values and redox potentials in the bovine Rieske iron-sulfur protein

21 January 2018

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Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics

21 January 2018

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Recent advances in implicit solvent-based methods for biomolecular simulations

21 January 2018

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Biomolecular simulations at constant pH.

21 January 2018

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Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

21 January 2018

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Free energy via molecular simulation: applications to chemical and biomolecular systems

21 January 2018

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Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

21 January 2018

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Redox-linked protonation state changes in cytochrome bc1 identified by Poisson–Boltzmann electrostatics calculations

21 January 2018

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Effect of HPr phosphorylation on structure, dynamics, and interactions in the course of transcriptional control

21 January 2018

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21 January 2018

Identifiers

DOI

10.1002/JCC.22919

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27 March 2017

DBLP publication ID

journals/jcc/UllmannU12

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DBLP Dataset 2021-01-02