相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory
Lieyang Chen et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2021)
Proton exit pathways surrounding the oxygen evolving complex of photosystem II
Divya Kaur et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2021)
Protein Motifs for Proton Transfers That Build the Transmembrane Proton Gradient
Divya Kaur et al.
FRONTIERS IN CHEMISTRY (2021)
Characterizing the Water Wire in the Gramicidin Channel Found by Monte Carlo Sampling Using Continuum Electrostatics and in Molecular Dynamics Trajectories with Conventional or Polarizable Force Fields
Yingying Zhang et al.
JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY (2021)
pKa Calculations with the Polarizable Drude Force Field and Poisson-Boltzmann Solvation Model
Alexey Aleksandrov et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Hydrogen bond network analysis reveals the pathway for the proton transfer in the E-channel of T. thermophilus Complex I
Umesh Khaniya et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2020)
Identifying the proton loading site cluster in the ba3 cytochrome c oxidase that loads and traps protons
Xiuhong Cai et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2020)
PypKa: A Flexible Python Module for Poisson-Boltzmann-Based pKa Calculations
Pedro B. P. S. Reis et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Bridge: A Graph-Based Algorithm to Analyze Dynamic H-Bond Networks in Membrane Proteins
Malte Siemers et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Network analysis of a proposed exit pathway for protons to the P-side of cytochrome c oxidase
Xiuhong Cai et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2018)
The Enthalpy-entropy Compensation Phenomenon. Limitations for the Use of Some Basic Thermodynamic Equations
Sergei Khrapunov
CURRENT PROTEIN & PEPTIDE SCIENCE (2018)
Reservoir pH replica exchange
Ana Damjanovic et al.
JOURNAL OF CHEMICAL PHYSICS (2018)
Replica-Exchange and Standard State Binding Free Energies with Grand Canonical Monte Carlo
Gregory A. Ross et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Ward Clustering Improves Cross-Validated Markov State Models of Protein Folding
Brooke E. Husic et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems
Brian K. Radak et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2017)
A Hybrid Molecular Dynamics/Multiconformer Continuum Electrostatics (MD/MCCE) Approach for the Determination of Surface Charge of Nanomaterials
Jiewei Hong et al.
JOURNAL OF PHYSICAL CHEMISTRY C (2017)
L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH
Andrew M. Intlekofer et al.
NATURE CHEMICAL BIOLOGY (2017)
Symmetry-related proton transfer pathways in respiratory complex I
Andrea Di Luca et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Two CI Ions and a Glu Compete for a Helix Cage in the CLC Proton/Cl- Antiporter
Cat Chenal et al.
BIOPHYSICAL JOURNAL (2017)
DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs
Lin Wang et al.
BIOINFORMATICS (2016)
Grotthuss mechanisms: from proton transport in proton wires to bioprotonic devices
Takeo Miyake et al.
JOURNAL OF PHYSICS-CONDENSED MATTER (2016)
New Perspectives on Proton Pumping in Cellular Respiration
Marten Wikstrom et al.
CHEMICAL REVIEWS (2015)
Enthalpy-Entropy Compensation upon Molecular Conformational Changes
Mazen Ahmad et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)
Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo
Gregory A. Ross et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
Jason M. Swails et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Proton transfer reactions and hydrogen-bond networks in protein environments
Hiroshi Ishikita et al.
JOURNAL OF THE ROYAL SOCIETY INTERFACE (2014)
Molecular mechanisms for generating transmembrane proton gradients
M. R. Gunner et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2013)
Adaptive spectral clustering with application to tripeptide conformation analysis
Fiete Haack et al.
JOURNAL OF CHEMICAL PHYSICS (2013)
H++3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations
Ramu Anandakrishnan et al.
NUCLEIC ACIDS RESEARCH (2012)
PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions
Mats H. M. Olsson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
MCCE analysis of the pKas of introduced buried acids and bases in staphylococcal nuclease
M. R. Gunner et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Progress in the prediction of pKa values in proteins
Emil Alexov et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding
Boris Aguilar et al.
BIOPHYSICAL JOURNAL (2010)
MCCE2: Improving Protein pKa Calculations with Extensive Side Chain Rotamer Sampling
Yifan Song et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)
Proton-Transfer Pathways in Photosynthetic Reaction Centers Analyzed by Profile Hidden Markov Models and Network Calculations
Eva-Maria Krammer et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
Using Multiconformation Continuum Electrostatics to Compare Chloride Binding Motifs in α-Amylase, Human Serum Albumin, and Omp32
Yifan Song et al.
JOURNAL OF MOLECULAR BIOLOGY (2009)
Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms
Jianyin Shao et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2007)
Statistical aspects of van't Hoff analysis: a simulation study
Andrei Zhukov et al.
JOURNAL OF MOLECULAR RECOGNITION (2007)
Atypical protonation states in the active site of HIV-1 protease: A computational study
Paul Czodrowski et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2007)
Protonation changes upon ligand binding to trypsin and thrombin: Structural interpretation based on pKa calculations and ITC experiments
Paul Czodrowski et al.
JOURNAL OF MOLECULAR BIOLOGY (2007)
Chance and design - Proton transfer in water, channels and bioenergetic proteins
Colin A. Wraight
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2006)
Are acidic and basic groups in buried proteins predicted to be ionized?
J Kim et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Improving implicit solvent simulations: a Poisson-centric view
NA Baker
CURRENT OPINION IN STRUCTURAL BIOLOGY (2005)
Valence and anion binding of bovine ribonuclease A between pH 6 and 8
TP Moody et al.
ANALYTICAL BIOCHEMISTRY (2005)
Estimating entropies from molecular dynamics simulations
C Peter et al.
JOURNAL OF CHEMICAL PHYSICS (2004)
Electrostatic analysis of the hepatitis C virus NS3 helicase reveals both active and allosteric site locations
DN Frick et al.
NUCLEIC ACIDS RESEARCH (2004)
A new method to evaluate the similarity of chromatographic fingerprints: Weighted Pearson product-moment correlation coefficient
YS Liu et al.
JOURNAL OF CHROMATOGRAPHIC SCIENCE (2004)
On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
RM Levy et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2003)
Extending the applicability of the nonlinear Poisson-Boltzmann equation: Multiple dielectric constants and multivalent ions
W Rocchia et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2001)
Modeling the effects of mutations on the free energy of the first electron transfer from QA- to QB in photosynthetic reaction centers
E Alexov et al.
BIOCHEMISTRY (2000)
Proton and electron transfer in bacterial reaction centers
MY Okamura et al.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS (2000)
分享论文
