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JOURNAL OF CHEMICAL THEORY AND COMPUTATION, ISSN 1549-9618, 02/2011, Volume 7, Issue 2, pp. 525 - 537
In this study, we have revised the rules and parameters for one of the most commonly used empirical pK(a) predictors, PROPKA, based on better physical... 
ELECTROSTATIC INTERACTIONS | A BETA-LACTAMASES | DIELECTRIC-CONSTANTS | MODELS | PKA | RATIONALIZATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | PROTEIN TITRATION CURVES | PROTON-BINDING | VALUES | CONTINUUM ELECTROSTATICS
Journal Article
Proteins: Structure, Function and Bioinformatics, ISSN 0887-3585, 12/2011, Volume 79, Issue 12, pp. 3333 - 3345
In this study, we validate and probe the description of electrostatic interactions within proteins by predicting and comparing pK(a) values of ionizable groups... 
Validation | PROPKA | Null-model | Homology modeling | Reorganization | Staphylococcal nuclease | Relative rmsd | DIELECTRIC-CONSTANTS | BIOCHEMISTRY & MOLECULAR BIOLOGY | relative rmsd | homology modeling | BIOPHYSICS | staphylococcal nuclease | INTERIOR | RATIONALIZATION | VALUES | reorganization | IONIZATION | validation | ASP
Journal Article
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, ISSN 1549-9618, 07/2011, Volume 7, Issue 7, pp. 2284 - 2295
The new empirical rules for protein pK(a) predictions implemented in the PROPKA3.0 software package (Olsson et al. J. Chem. Theory Comput. 2010, 7, 525-537)... 
ACTIVE-SITE | PLASMODIUM-FALCIPARUM | HYDROXYNITRILE LYASE | NUCLEAR-MAGNETIC-RESONANCE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | DIHYDROFOLATE-REDUCTASE | CHEMISTRY, PHYSICAL | CRYSTAL-STRUCTURES | ESCHERICHIA-COLI THIOREDOXIN | HIV-1 PROTEASE | HEVEA-BRASILIENSIS | ASPARTIC PROTEINASE
Journal Article
LANGMUIR, ISSN 0743-7463, 06/2014, Volume 30, Issue 22, pp. 6437 - 6445
We have used density functional theory and the implicit solvent model, COSMO-RS, to investigate how the acidity constant, pK(a) of organic acids and bases... 
ENERGY | SELF-ASSEMBLED MONOLAYERS | MATERIALS SCIENCE, MULTIDISCIPLINARY | CHEMICAL FORCE MICROSCOPY | CHEMISTRY, PHYSICAL | SURFACE PK(A) | CHEMISTRY, MULTIDISCIPLINARY | RECOVERY | BASIS-SETS | VALUES | COSMO-RS | ELECTROSTATICS | PROTEINS
Journal Article
Journal of Molecular Modeling, ISSN 1610-2940, 03/2012, Volume 18, Issue 3, pp. 1097 - 1106
Unlike atomistic and continuum models, empirical pk(a) predicting methods need to include desolvation contributions explicitly. This study describes a new... 
Protein modeling | Solvation | PROPKA | Desolvation | ENERGY | BIOCHEMISTRY & MOLECULAR BIOLOGY | PKA | CHEMISTRY, MULTIDISCIPLINARY | MOLECULAR-MECHANICS | PREDICTION | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | BIOPHYSICS | RATIONALIZATION | pK(a) | VALUES
Journal Article
Energy and Fuels, ISSN 0887-0624, 07/2016, Volume 30, Issue 7, pp. 5346 - 5354
Core plug and field tests have shown that significantly more oil can be produced from sandstone reservoirs when the water that is injected to maintain pressure... 
ENGINEERING, CHEMICAL | OIL-RECOVERY | CHALK | WETTABILITY | ENERGY & FUELS | ATOMIC-FORCE MICROSCOPE
Journal Article
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0002-7863, 11/2004, Volume 126, Issue 46, pp. 15167 - 15179
Journal Article
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, ISSN 0027-8424, 06/2007, Volume 104, Issue 23, pp. 9661 - 9666
The catalytic power of enzymes containing coenzyme B-12 cofactor has been, in some respects, the "last bastion" for the strain hypothesis. The present work... 
ENZYMATIC-REACTIONS | transition state stabilization | simulation of enzymatic reactions | METHYLMALONYL-COA MUTASE | STABILIZATION | MULTIDISCIPLINARY SCIENCES | GLUTAMATE MUTASE | MECHANICS | C BOND | COENZYME B-12 | CHEMISTRY | strain effect | BINDING | INSIGHTS
Journal Article
Journal of Physical Chemistry C, ISSN 1932-7447, 11/2017, Volume 121, Issue 43, pp. 24025 - 24035
Density functional theory (DFT) with semiempirical dispersion corrections (DFT-D2) has been used to calculate the binding energy of a CO2 molecule on the... 
MATERIALS SCIENCE, MULTIDISCIPLINARY | SURFACE-STRUCTURE | TEMPERATURE CONDITIONS | CHEMISTRY, PHYSICAL | INTERFACIAL-TENSION | NANOSCIENCE & NANOTECHNOLOGY | FUNCTIONAL-GROUP ADSORPTION | ATOMISTIC SIMULATION | GEOLOGICAL SEQUESTRATION | 10OVER-BAR4 SURFACE | MOLECULAR-DYNAMICS SIMULATIONS | CARBON-DIOXIDE | FREE-ENERGY
Journal Article
International Journal of Quantum Chemistry, ISSN 0020-7608, 2001, Volume 81, Issue 5, pp. 335 - 347
Journal Article
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0002-7863, 08/2001, Volume 123, Issue 32, pp. 7866 - 7876
The dimeric CUA Site found in cytochrome c oxidase and nitrous oxide reductase has been studied with the density functional B3LYP method. We have optimized the... 
CONTINUUM APPROXIMATION | MIXED-VALENCE | ELECTRON-TRANSFER CENTER | SPECTROSCOPIC PROPERTIES | SOLVATION ENERGY | BLUE-COPPER PROTEINS | CYTOCHROME-OXIDASE | NITROUS-OXIDE REDUCTASE | THERMUS-THERMOPHILUS | CHEMISTRY, MULTIDISCIPLINARY | SIMPLE COMPUTATIONAL MODEL
Journal Article
Langmuir, ISSN 0743-7463, 04/2015, Volume 31, Issue 13, pp. 3847 - 3853
Molecular dynamics (MD) simulations were used to explore adsorption on calcite, from a 1:1 mixture of ethanol and water, on planar {10.4} and stepped, i.e.... 
CRYSTALLIZATION | BIOMINERALIZATION | MATERIALS SCIENCE, MULTIDISCIPLINARY | CHEMISTRY, PHYSICAL | GROMACS | CHEMISTRY, MULTIDISCIPLINARY | ATOMISTIC SIMULATION | DISSOLUTION | INTERFACE | MODELS | MOLECULAR-DYNAMICS SIMULATIONS | ENERGIES | MORPHOLOGY
Journal Article
BMC Structural Biology, ISSN 1472-6807, 2011, Volume 11, Issue 1, pp. 6 - 6
Background: Charge states of ionizable residues in proteins determine their pH-dependent properties through their pK(a) values. Thus, various theoretical... 
VALUES | BIOPHYSICS | RESIDUES | STABILITY | RATIONALIZATION | Models, Molecular | Software | Proteins - chemistry | Models, Chemical | Computer Simulation | Hydrogen-Ion Concentration | Proteins | Usage | Research | Properties | Hydrogen-ion concentration | Studies | Software packages | User interface | Manuscripts | Programming languages
Journal Article
Langmuir, ISSN 0743-7463, 2013, Volume 29, Issue 35, pp. 11062 - 11073
The adsorption behavior of calcium carbonate is an important factor in many processes in nature, industry, and biological systems. We determined and compared... 
CRYSTALLIZATION | TRANSFORMATION | ACID | MATERIALS SCIENCE, MULTIDISCIPLINARY | SURFACE-STRUCTURE | CHEMISTRY, PHYSICAL | SIMULATION | CHEMISTRY, MULTIDISCIPLINARY | DISTRIBUTIONS | ETHANOL | BIOLOGICAL-CONTROL | ISOSTERIC HEAT | WATER
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 03/2004, Volume 126, Issue 9, pp. 2820 - 2828
Journal Article
Scientific Reports, ISSN 2045-2322, 12/2017, Volume 7, Issue 1, pp. 7592 - 11
Journal Article
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