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Journal of Chemical Theory and Computation, ISSN 1549-9618, 05/2019, Volume 15, Issue 5, pp. 2896 - 2912
A spatially resolved version of the density-functional method for solvation thermodynamics is presented by extending the free-energy functional previously... 
MOLECULAR-DYNAMICS | EXPLICIT SOLVENT | HYDRATION SHELL | THERMODYNAMICS | PROTEIN | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | REPRESENTATION | CHEMISTRY, PHYSICAL | FORCE-FIELD | BINDING | ALANINE DIPEPTIDE | WATER | Thermodynamics | Solvents | Alanine | Solvation | Flux density | Energy | Hydrogen bonds | Decomposition | Representations | Free energy | Hydroxyl groups
Journal Article
ACS Catalysis, ISSN 2155-5435, 08/2018, Volume 8, Issue 8, pp. 6908 - 6913
Insights into the mechanism of the catalytic cycle for methanol dehydrogenation catalyzed by a highly active PNP pincer ruthenium complex in methanol solvent... 
LIGAND BIFUNCTIONAL CATALYSIS | MECHANISM | CO2 | CHEMISTRY, PHYSICAL | molecular dynamics | H-2 | ALCOHOLS | KETONES | explicit solvent | C-H activation | EVOLUTION | density functional theory | PINCER COMPLEXES | H-2 formation | CARBON-DIOXIDE | methanol dehydrogenation | WATER | H2 formation | C−H activation
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 02/2019, Volume 123, Issue 5, pp. 957 - 973
In this study, the electronic properties of bioactive proteins were analyzed using an ab initio fragment molecular orbital (FMO) methodology in solution:... 
EXPLICIT SOLVENT | CRYSTAL-STRUCTURE | FMO CALCULATIONS | DNA | ESTROGEN-RECEPTOR-ALPHA | CHEMISTRY, PHYSICAL | QUANTUM-MECHANICAL DESCRIPTION | APPROXIMATE COMPUTATIONAL METHOD | ENERGIES | POTENT INHIBITORS | FUNCTIONAL TIGHT-BINDING
Journal Article
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, ISSN 1549-9618, 08/2019, Volume 15, Issue 8, pp. 4623 - 4631
A model for carboxylic acids, in both the protonated and deprotonated states, is developed in which hydrogen interaction sites are not used and all... 
WATER MODEL | MOLECULAR-DYNAMICS | EXPLICIT SOLVENT | SENSITIVE LIPOSOMES | CONDENSED PHASES | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | CONFORMATION | POLY(METHACRYLIC ACID) | IONIZATION | HYDRATION | AQUEOUS-SOLUTION | Methacrylic acid | Protonation | Carboxylic acids | Computer simulation | Polymers
Journal Article
PROTEIN SCIENCE, ISSN 0961-8368, 11/2018, Volume 27, Issue 11, pp. 1910 - 1922
The estimation of changes in free energy upon mutation is central to the problem of protein design. Modern protein design methods have had remarkable success... 
BINDING FREE-ENERGY | ALPHA-HELIX | STABILITY | BIOCHEMISTRY & MOLECULAR BIOLOGY | PH MOLECULAR-DYNAMICS | catalysis | binding | PARTICLE MESH EWALD | RELIABLE PREDICTION | molecular dynamics | SIMULATION | EXPLICIT SOLVENT | COMPUTATIONAL DESIGN | protein folding | EFFICIENT
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 09/2016, Volume 12, Issue 9, pp. 4662 - 4673
Methods for the calculation of the pK a ionizable amino acids are valuable tools for understanding pH-dependent properties of proteins. Cysteine is unique... 
METHIONINE SULFOXIDE REDUCTASE | EXPLICIT SOLVENT | ACTIVE-SITE | INDUCED CONFORMATIONAL TRANSITION | CRYSTAL-STRUCTURE | MUSCLE CREATINE-KINASE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE METHOD | MOLECULAR-DYNAMICS SIMULATIONS | FREE-ENERGY | TYROSINE-PHOSPHATASE
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 10/2016, Volume 120, Issue 41, pp. 10635 - 10648
Classical force field (FF) molecular dynamics (MD) simulations of RNA tetranucleotides have substantial problems in reproducing conformer populations indicated... 
AUXILIARY BASIS-SETS | MOLECULAR-DYNAMICS | STRUCTURAL BIOLOGY | EXPLICIT-SOLVENT | CHEMISTRY, PHYSICAL | PARTICLE MESH EWALD | QUANTUM-CHEMICAL COMPUTATIONS | FREE-ENERGIES | HARTREE-FOCK | PHOSPHATE BACKBONE | NUCLEIC-ACIDS | Molecular simulation | Usage | Research | RNA | Quantum theory
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 06/2018, Volume 14, Issue 6, pp. 3289 - 3297
The pH (low) insertion peptides (pHLIPs) is a family of peptides that are able to insert into a lipid bilayer at acidic pH. The molecular mechanism of pHLIPs... 
EXPLICIT SOLVENT | WATER MODELS | LIPID-BILAYERS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | PH MOLECULAR-DYNAMICS | LOW INSERTION PEPTIDE | CHEMISTRY, PHYSICAL | CONSTANT-PH | MD SIMULATIONS | PROTEINS | DISCRETE PROTONATION STATES | TRANSMEMBRANE HELIX
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 05/2011, Volume 133, Issue 17, pp. 6809 - 6816
Journal Article
Molecular Physics, ISSN 0026-8976, 10/2012, Volume 110, Issue 19-20, pp. 2401 - 2412
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 05/2018, Volume 122, Issue 19, pp. 5030 - 5037
Enveloping distribution sampling (EDS) is an efficient approach to calculate multiple free-energy differences from a single molecular dynamics (MD) simulation.... 
EXPLICIT SOLVENT | ONE-STEP PERTURBATION | EDS | IMPLEMENTATION | CHEMISTRY, PHYSICAL | FORCE-FIELD | LIGAND-BINDING DOMAIN | MOLECULAR-DYNAMICS SIMULATIONS | EXCHANGE | EFFICIENT | SINGLE SIMULATION
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 06/2017, Volume 38, Issue 15, pp. 1260 - 1269
BACE1 is a major therapeutic target for prevention and treatment of Alzheimer's disease. Developing inhibitors that can selectively target BACE1 in favor of... 
protease | molecular dynamics | drug design | Alzheimer's disease | protein‐ligand binding | protein electrostatics | protein-ligand binding | BETA-SECRETASE | D DEFICIENCY | FORCE-FIELDS | SIMULATION | CHEMISTRY, MULTIDISCIPLINARY | EXPLICIT SOLVENT | PROTON TAUTOMERISM | AMYLOID-BETA | PARTICLE-MESH EWALD | PROTEINS | Index Medicus
Journal Article
JOURNAL OF CHEMICAL INFORMATION AND MODELING, ISSN 1549-9596, 07/2017, Volume 57, Issue 7, pp. 1548 - 1562
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 04/2010, Volume 31, Issue 6, pp. 1268 - 1272
We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for... 
explicit solvent | graphics processing unit | cutoff | reaction field | molecular dynamics | GPU | nonbonded | water | Water | Cutoff | Explicit solvent | Molecular dynamics | Nonbonded | Reaction field | Graphics processing unit | LAMBDA-REPRESSOR | SIMULATIONS | CHEMISTRY, MULTIDISCIPLINARY | Algorithms | Lipid Bilayers - chemistry | Proteins - chemistry | Molecular Dynamics Simulation
Journal Article
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, ISSN 1549-9618, 04/2019, Volume 15, Issue 4, pp. 2392 - 2419
A new method is proposed to calculate alchemical free-energy differences based on molecular dynamics (MD) simulations, called the conveyor belt thermodynamic... 
MONTE-CARLO | EQUATION-OF-STATE | RELATIVE FREE-ENERGIES | EXPLICIT-SOLVENT | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | FORCE-FIELD | EXCHANGE MOLECULAR-DYNAMICS | LOCAL ELEVATION | SIDE-CHAIN ANALOGS | PERTURBATION CALCULATIONS | PARALLEL-TEMPERING SIMULATIONS
Journal Article
Biophysical Journal, ISSN 0006-3495, 08/2013, Volume 105, Issue 4, pp. L15 - L17
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 09/2015, Volume 119, Issue 38, pp. 12355 - 12364
The Varkud Satellite RNA contains a self-cleaving ribozyme that has been shown to function independently of its surroundings. This 160 nucleotide ribozyme... 
BIOMOLECULAR SIMULATIONS | RIBOZYME | EXPLICIT SOLVENT | AMBER | CHEMISTRY, PHYSICAL | FORCE-FIELD | PARTICLE MESH EWALD | MOLECULAR-DYNAMICS SIMULATIONS | EXCHANGE | NEUROSPORA | SUBSTRATE RECOGNITION | Molecular simulation | Usage | RNA | Analysis | Molecular dynamics | Nuclear magnetic resonance spectroscopy | Research
Journal Article
Current Topics in Medicinal Chemistry, ISSN 1568-0266, 2017, Volume 17, Issue 23, pp. 2617 - 2625
Bio-molecular dynamics (MD) simulations based on graphical processing units (GPUs) were first released to the public in the early 2009 with the code ACEMD.... 
Perspective | Simulation | Molecular dynamics | ACEMD | Drug discovery | Review | GPU | CHEMISTRY, MEDICINAL | DOCKING | GPCR-LIGAND RECOGNITION | TIME-SCALE | EXPLICIT SOLVENT | PARAMETERIZATION | FORCE-FIELD | SIMULATIONS | PROTEINS | FREE-ENERGY | BINDING | Time | Sampling | Graphics processing units
Journal Article
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