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Current Opinion in Structural Biology, ISSN 0959-440X, 02/2013, Volume 23, Issue 1, pp. 58 - 65
► Millisecond simulations. ► Hardware and software advances. ► Simulation to understanding. Quantitatively accurate all-atom molecular dynamics (MD)... 
PATHWAYS | SPEED LIMIT | MODELS | EXPLICIT-SOLVENT | KINETICS | BIOCHEMISTRY & MOLECULAR BIOLOGY | TRP-CAGE | BIOMOLECULAR SIMULATION | MOLECULAR-DYNAMICS SIMULATIONS | FORCE-FIELDS | EFFICIENT | CELL BIOLOGY | Kinetics | Proteins - chemistry | Molecular Dynamics Simulation | Protein Folding
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 08/2008, Volume 29, Issue 11, pp. 1859 - 1865
Journal Article
by Jo, S and Kim, T and Iyer, VG and Im, W
JOURNAL OF COMPUTATIONAL CHEMISTRY, ISSN 0192-8651, 08/2008, Volume 29, Issue 11, pp. 1859 - 1865
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 02/2018, Volume 115, Issue 7, pp. E1346 - E1355
Molecular dynamics (MD) simulation has become a powerful tool for characterizing at an atomic level of detail the conformational changes undergone by proteins.... 
molecular dynamics simulations | Anton | force field | AMBER | Nucleic acid | SIDE-CHAIN | MULTIDISCIPLINARY SCIENCES | ION PARAMETERS | DISORDERED PROTEIN | nucleic acid | NUCLEIC-ACIDS | STACKING | NMR | EXPLICIT-SOLVENT | MOLECULAR-DYNAMICS SIMULATIONS | EXCHANGE | WATER | Physical Sciences | PNAS Plus
Journal Article
The Journal of Physical Chemistry Letters, ISSN 1948-7185, 05/2014, Volume 5, Issue 10, pp. 1771 - 1782
We present a brief overview of explicit solvent molecular dynamics (MD) simulations of nucleic acids. We explain physical chemistry limitations of the... 
MATERIALS SCIENCE, MULTIDISCIPLINARY | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | NANOSCIENCE & NANOTECHNOLOGY | EXPLICIT SOLVENT | AMBER FORCE-FIELD | QUADRUPLEX DNA | REPLICA-EXCHANGE METHOD | TRANSFER-RNA | HDV RIBOZYME | BINDING-SITES | DELTA-VIRUS RIBOZYME | ENERGY LANDSCAPE | STRUCTURAL DYNAMICS
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 11/2007, Volume 3, Issue 6, pp. 2312 - 2334
Molecular dynamics simulation methods produce trajectories of atomic positions (and optionally velocities and energies) as a function of time and provide a... 
EXPLICIT SOLVENT | FOLDING SIMULATIONS | PROTEIN CONFORMATIONAL SPACE | CONTINUUM SOLVENT | INTEGRASE CATALYTIC CORE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | COMPUTER-SIMULATION | HIV-1 PROTEASE | EQUILIBRIUM SIMULATIONS | NUCLEIC-ACIDS | MINOR-GROOVE
Journal Article
Journal Article
Physical Chemistry Chemical Physics, ISSN 1463-9076, 2/2015, Volume 17, Issue 9, pp. 6174 - 6191
Journal Article
Physical chemistry chemical physics : PCCP, ISSN 1463-9076, 03/2015, Volume 17, Issue 9, pp. 6174 - 6191
Over the past decade, pharmaceutical companies have seen a decline in the number of drug candidates successfully passing through clinical trials, though... 
Thermodynamics | Models, Chemical | Solubility | Solutions - chemistry
Journal Article
Biophysical Journal, ISSN 0006-3495, 04/2018, Volume 114, Issue 8, pp. 1776 - 1790
Nucleic acids generally reside in cellular aqueous solutions with mixed divalent/monovalent ions, and the competitive binding of divalent and monovalent ions... 
POISSON-BOLTZMANN APPROACH | MONTE-CARLO | SOLVENT SIMULATIONS | BIOMOLECULAR SIMULATIONS | BIOPHYSICS | DNA OLIGOMERS | EXPLICIT-SOLVENT | SALT CONCENTRATION | MOLECULAR-DYNAMICS SIMULATIONS | METAL-IONS | FREE-ENERGY | Nucleic Acids and Genome Biophysics
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 10/2006, Volume 128, Issue 41, pp. 13435 - 13441
We develope a new free-energy method, based on the combination of parallel tempering and metadynamics, and apply this method to the calculation of the... 
EXPLICIT SOLVENT | THERMODYNAMICS | KINETICS | PROTEIN-G | FRAGMENT | EXCHANGE MOLECULAR-DYNAMICS | MODEL | SIMULATION | CHEMISTRY, MULTIDISCIPLINARY | AQUEOUS-SOLUTION | WATER | Thermodynamics | Algorithms | Hydrogen Bonding | Peptides - chemistry | Protein Structure, Secondary | Computer Simulation | Water - chemistry | Protein Conformation | Protein Folding
Journal Article
Nature Physics, ISSN 1745-2473, 10/2010, Volume 6, Issue 10, pp. 751 - 758
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 03/2014, Volume 10, Issue 3, pp. 934 - 941
We show that an Ng bridge function modified version of the three-dimensional reference interaction site model (3D-RISM-NgB) solvation free energy method can... 
HYDRATION FREE-ENERGIES | AMBIENT AQUEOUS-SOLUTION | EXPLICIT SOLVENT | LIGAND-BINDING | IMPLICIT-SOLVENT MODEL | MEAN FORCE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | EFFICIENT GENERATION | INTEGRAL-EQUATION THEORY | INTERACTION SITE MODEL | FAVORABLE BINDING-SITES
Journal Article
Current Opinion in Colloid & Interface Science, ISSN 1359-0294, 2008, Volume 13, Issue 6, pp. 376 - 388
Charged polymers are macromolecules with ionizable groups. These polymeric systems demonstrate unique properties that are qualitatively different from their... 
EXPLICIT SOLVENT | MEAN-FIELD THEORY | SHORT-RANGE INTERACTIONS | COUNTERION-CONDENSATION | CHEMISTRY, PHYSICAL | FLEXIBLE POLYELECTROLYTES | MONTE-CARLO-SIMULATION | MOLECULAR-DYNAMICS SIMULATIONS | DIBLOCK POLYAMPHOLYTE SOLUTIONS | LINKED POLYELECTROLYTE GELS | STIFF-CHAIN POLYELECTROLYTES
Journal Article