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ORGANIC LETTERS, ISSN 1523-7060, 07/2019, Volume 21, Issue 13, pp. 5243 - 5247
Confinement provided by the reaction space alters the photostationary state isomer distribution during the geometric isomerization of excited... 
PHOTOCHEMICAL REACTIVITY | ORGANIC-MOLECULES | ENERGY | POLYENES | CAPSULEPLEX | PHOTOISOMERIZATION | ASYMMETRIC INDUCTION | LAMBDA-DYNAMICS | CHEMISTRY, ORGANIC | EFFICIENT | WATER
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 07/2018, Volume 122, Issue 29, pp. 7219 - 7232
In this study, a combined molecular docking (rigid and flexible) and all-atom molecular dynamics simulations technique have been employed to investigate... 
MOLECULAR-INTERACTIONS | HUMAN SERUM-ALBUMIN | LAMBDA-DYNAMICS | HYDROLYSIS | REACTIVITY | CHEMISTRY, PHYSICAL | FORCE-FIELD | IDENTIFICATION | SIMULATION | MASS-SPECTROMETRY | AQUEOUS-SOLUTION
Journal Article
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, ISSN 1463-9076, 03/2019, Volume 21, Issue 10, pp. 5499 - 5509
In this study, interactions of the catalytically active binuclear form of glycerophosphodiesterase (GpdQ) with four chemically diverse substrates, i.e. NPP (a... 
PURPLE ACID-PHOSPHATASE | PHOSPHOTRIESTERASE | BIOREMEDIATOR GLYCEROPHOSPHODIESTERASE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | ORGANOPHOSPHATE-DEGRADING ENZYME | LAMBDA-DYNAMICS | REACTIVITY | CHEMISTRY, PHYSICAL | SIMULATION | BINDING | EFFICIENT | CATALYTIC MECHANISMS
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 04/2015, Volume 119, Issue 13, pp. 4601 - 4607
In this work, we apply the recently developed constant pH molecular dynamics technique to study protonation equilibria of titratable side chains in the context... 
FREE-ENERGY CALCULATIONS | LIPID-BILAYERS | SOLID-STATE NMR | IMPLICIT MEMBRANE | PH MOLECULAR-DYNAMICS | LAMBDA-DYNAMICS | CHEMISTRY, PHYSICAL | CONSTANT-PH | COMPUTER-SIMULATIONS | ARGININE SIDE-CHAIN | HYDROPHOBIC MISMATCH
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 03/2012, Volume 8, Issue 3, pp. 810 - 823
The orthogonal space random walk (OSRW) method, which enables synchronous acceleration of the motions of a focused region and its coupled environment, was... 
MONTE-CARLO | THERMODYNAMIC INTEGRATION | ELECTRON-TRANSFER | RANDOM-WALK | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | LAMBDA-DYNAMICS | CHEMISTRY, PHYSICAL | SYSTEMS | LIGAND | MOLECULAR-DYNAMICS SIMULATIONS | FORCE-FIELDS | CHARMM
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY C, ISSN 1932-7447, 05/2016, Volume 120, Issue 18, pp. 10041 - 10050
The pK(a) of the p-mercaptobenzoic acid (pMBA) ligands in the Au-102(pMBA)(44) nanocluster was measured by using acid base and IR titration. The observed... 
NMR-SPECTROSCOPY | MATERIALS SCIENCE, MULTIDISCIPLINARY | PH MOLECULAR-DYNAMICS | PROTECTED GOLD NANOCLUSTERS | CHEMISTRY, PHYSICAL | NANOSCIENCE & NANOTECHNOLOGY | ENHANCED RAMAN-SCATTERING | 4-MERCAPTOBENZOIC ACID | FREE-ENERGY CALCULATIONS | NANOPARTICLES | LIPID-BILAYERS | LAMBDA-DYNAMICS | AU-144 CLUSTERS
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 2005, Volume 122, Issue 14, pp. 144107 - 144107
Recent work has demonstrated the Bennett acceptance ratio method is the best asymptotically unbiased method for determining the equilibrium free energy between... 
PATH | MOLECULAR SIMULATION | EQUILIBRIUM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | LAMBDA-DYNAMICS | CHEMISTRY, PHYSICAL | POTENTIAL FUNCTIONS | PERTURBATION CALCULATIONS | HISTOGRAM ANALYSIS METHOD | SINGLE SIMULATION | HYDRATION | ACCURACY | Models, Theoretical | Thermodynamics | Energy Transfer | Bias | Computer Simulation | Index Medicus
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 2017, Volume 13, Issue 1, pp. 210 - 222
Journal Article
Journal of Computer-Aided Molecular Design, ISSN 0920-654X, 01/2018, Volume 32, Issue 1, pp. 89 - 102
The opportunity to prospectively predict ligand bound poses and free energies of binding to the Farnesoid X Receptor in the D3R Grand Challenge 2 provided a... 
CDOCKER | Protein-ligand docking | D3R | Free energy calculation | λ dynamics | Drug design data resources | Docking | Ligands | Dynamics | Computer aided design--CAD | Crystallography | Free energy | Index Medicus | Protein-ligand Docking | Free Energy Calculation | lambda dynamics | Drug Design Data Resources
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 11/2016, Volume 12, Issue 11, pp. 5411 - 5421
Journal Article
Biophysical Journal, ISSN 0006-3495, 07/2014, Volume 107, Issue 1, pp. 76 - 87
The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility... 
PURPLE MEMBRANE | BIOPHYSICS | INTERFACIAL WATER | PHOSPHATIDYLCHOLINE BILAYERS | LAMBDA-DYNAMICS | NACL | CONSTANT-PRESSURE | MOLECULAR-DYNAMICS SIMULATIONS | PHOSPHOLIPID-BILAYERS | PLASMA-MEMBRANE | BIOLOGICAL-MEMBRANES | Protons | Lipid Bilayers - chemistry | Diffusion | Dimyristoylphosphatidylcholine - chemistry | Lipids | Biophysics | Index Medicus | Channels and Transporters
Journal Article
RSC ADVANCES, ISSN 2046-2069, 2017, Volume 7, Issue 32, pp. 20007 - 20014
The pK(a) of a polyelectrolyte has been determined experimentally by potentiometric titration and computed using Molecular Dynamics (MD) constant pH (CpH)... 
MONTE-CARLO | SURFACE-PROPERTIES | PH-RESPONSIVE POLYMERS | GENE DELIVERY | DRUG-DELIVERY | LAMBDA-DYNAMICS | CONSTANT-PH | PROTEINS | CHEMISTRY, MULTIDISCIPLINARY | SENSITIVE POLYMERS | TITRATING POLYELECTROLYTES
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 03/2018, Volume 14, Issue 3, pp. 1564 - 1582
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 12/2016, Volume 145, Issue 23, pp. 234109 - 234109
Single-step free energy perturbation (sFEP) has often been proposed as an efficient tool for a quick free energy scan due to its straightforward protocol and... 
HYDRATION FREE-ENERGIES | STATISTICAL-MECHANICS | MOLECULAR-DYNAMICS | LIGAND-BINDING | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | LAMBDA-DYNAMICS | CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE | FORCE-FIELD | SIMULATIONS | BINDING FREE-ENERGIES | LIPID-BILAYER | Ethylbenzene | Mathematical analysis | Anisole | Benzene | Molecular dynamics | Ligands | Transformations | Sampling | Free energy
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 07/2013, Volume 9, Issue 7, pp. 3136 - 3150
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 12/2017, Volume 147, Issue 21, pp. 214902 - 214902
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 01/2012, Volume 8, Issue 1, pp. 36 - 46
Journal Article
The Journal of Chemical Physics, ISSN 0021-9606, 08/2018, Volume 149, Issue 7, pp. 072302 - 072302
For the high throughput design of protein:peptide binding, one must explore a vast space of amino acid sequences in search of low binding free energies. This... 
MONTE-CARLO | LIGAND-BINDING | ENERGY FUNCTIONS |