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Journal of Computational Chemistry, ISSN 0192-8651, 12/2013, Volume 34, Issue 32, pp. 2757 - 2770
Journal Article
NATURE, ISSN 0028-0836, 08/2015, Volume 524, Issue 7565, pp. 315 - 315
Activation of the mu-opioid receptor (mu OR) is responsible for the efficacy of the most effective analgesics. To shed light on the structural basis for mu OR... 
CRYSTALLIZING MEMBRANE-PROTEINS | COMPLEX | LIPIDIC MESOPHASES | PROTEIN-COUPLED RECEPTOR | MULTIDISCIPLINARY SCIENCES | FORCE-FIELD | ADRENERGIC-RECEPTOR | MOLECULAR-DYNAMICS SIMULATIONS | CHARMM | MICE LACKING | MUSCARINIC ACETYLCHOLINE-RECEPTOR
Journal Article
Organic and Biomolecular Chemistry, ISSN 1477-0520, 2019, Volume 17, Issue 25, pp. 6269 - 6276
In this work, molecular dynamics and QM/MM calculations were employed to examine the structural and catalytic features of the retaining glucosyltransferase... 
CHEMISTRY, ORGANIC | MOLECULAR-DYNAMICS | SPECIFICITY | SIMULATION | CHARMM | ENZYMES
Journal Article
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0002-7863, 01/2018, Volume 140, Issue 2, pp. 827 - 833
Peptoid polymers are often crystalline in the solid-state as examined by X-ray scattering, but thus far, there has been no attempt to identify a common... 
PERSISTENCE LENGTH | CRYSTALLIZATION | SECONDARY-STRUCTURE | BONDS | DYNAMICS | NANOSHEETS | SIMULATION | CHARMM | POLYPEPTOIDS | EFFICIENT | CHEMISTRY, MULTIDISCIPLINARY
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 01/2015, Volume 11, Issue 1, pp. 276 - 285
The weighted histogram analysis method (WHAM) is widely used to obtain accurate free energies from biased molecular simulations. However, WHAM free energies... 
MOLECULAR-DYNAMICS | MONTE-CARLO DATA | KINETICS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | SIMULATIONS | EXCHANGE | CHARMM | BAYESIAN-ANALYSIS
Journal Article
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, ISSN 0002-7863, 07/2019, Volume 141, Issue 26, pp. 10431 - 10439
The design of artificial enzymes is an emerging field of research. Although progress has been made, the catalytic proficiency of many designed enzymes is low... 
ALDOLASE | ENERGY | MECHANISM | COMPUTATIONAL DESIGN | CONFORMATIONAL DYNAMICS | MUTATIONS | SIMULATION | CHARMM | MOTIONS | CHEMISTRY, MULTIDISCIPLINARY | PROMOTING VIBRATION
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 08/2018, Volume 122, Issue 34, pp. 8185 - 8192
The outer membrane (OM) of Gram-negative bacteria is a unique asymmetric lipid bilayer containing lipopolysaccharides (LPS) in the outer leaflet and... 
PORIN | CHANNEL | SPECTROSCOPY | ESCHERICHIA-COLI | LIPOPOLYSACCHARIDE | CHEMISTRY, PHYSICAL | FORCE-FIELD | OPRP | GUI | CHARMM | MOLECULAR-DYNAMICS SIMULATION
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 10/2018, Volume 122, Issue 42, pp. 9713 - 9723
Amphipathic helices are key domains of peripheral membrane proteins, targeting specific membranes to enable proper protein function as well as changing the... 
TRANSPORT | CHOLESTEROL | MEMBRANE CURVATURE | HELICES | CHEMISTRY, PHYSICAL | FORCE-FIELD | SIMULATIONS | BILAYERS | CHARMM | OSBP-RELATED PROTEINS | FAMILY
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 03/2019, Volume 123, Issue 12, pp. 2697 - 2709
In addition to obtaining the highly precise volumes of lipids in lipid bilayers, it has been desirable to obtain the volumes of parts of each lipid, such as... 
GEL PHASE | UNSATURATED PHOSPHATIDYLCHOLINES | LECITHIN BILAYERS | CHEMISTRY, PHYSICAL | DIFFUSION | SIMULATIONS | ANGLE | CHARMM | WATER
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 05/2018, Volume 122, Issue 21, pp. 5308 - 5315
Insight into the molecular interactions of homotactic and heterotactic association of caffeine and pyridine in aqueous solution is given on the basis of both... 
GLUCOSE | LIQUID WATER | CHEMISTRY, PHYSICAL | SIMULATION | CHARMM | AGGREGATION | HYDRATION | AQUEOUS-SOLUTION | CHLORIDE | SURFACES
Journal Article
Biophysical Journal, ISSN 0006-3495, 12/2018, Volume 115, Issue 12, pp. 2403 - 2412
Peptides with the ability to bind and insert into the cell membrane have immense potential in biomedical applications. pH (low) insertion peptide (pHLIP), a... 
MOLECULAR-DYNAMICS | BIOPHYSICS | AMBER | MECHANISM | ENERGETICS | HELIX | PARTICLE MESH EWALD | GUI | SIMULATIONS | CHARMM | LIPID-BILAYER
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 10/2013, Volume 139, Issue 16, pp. 164106 - 164106
In molecular dynamics simulations, control over temperature and pressure is typically achieved by augmenting the original system with additional dynamical... 
THERMOSTAT | ALGORITHMS | CHARMM | GRAPHICS PROCESSING UNITS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | Artifacts | Temperature | Pressure | Molecular Dynamics Simulation | Index Medicus
Journal Article
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, ISSN 1549-9618, 10/2011, Volume 7, Issue 10, pp. 3379 - 3390
GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics simulation trajectories and as such is part of the GROningen MOlecular... 
PEPTIDES | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | FORCE-FIELD | SECONDARY STRUCTURE | MOLECULAR-DYNAMICS SIMULATIONS | PARAMETER SET | PROTEINS | CHARMM | FREE-ENERGY | SOLVATION | NUCLEIC-ACIDS
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 08/2019, Volume 123, Issue 33, pp. 7123 - 7136
Polysaccharide lyases (PLs) are an important class of proteins that are excreted from bacteria to degrade sugars in the extracellular matrix of the host. The... 
ALGINATE LYASE | MOLECULAR-DYNAMICS | ACID | SPECIFICITY | MECHANISM | CHEMISTRY, PHYSICAL | FORCE-FIELD | SIMULATION | CHARMM | GLYCAN READER | INSIGHTS | Index Medicus
Journal Article