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2014, Advances in experimental medicine and biology, ISBN 9400776055, Volume 797., xii, 139 pages
"The aim of this book volume is to explain the importance of Markov state models to molecular simulation, how they work, and how they can be applied to a range... 
Time Factors | Markov processes | Models, Molecular | Markov chains | Biology | Mathematical models | Molecular Dynamics Simulation | Biology-Mathematical models | Molecular dynamics
Book
Journal of the American Chemical Society, ISSN 0002-7863, 02/2018, Volume 140, Issue 7, pp. 2386 - 2396
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2013, Volume 9, Issue 4, pp. 2000 - 2009
Markov State Models (MSMs) provide an automated framework to investigate the dynamical properties of high-dimensional molecular simulations. These models can... 
ENSEMBLE | PATHWAYS | PROTEIN | FREE-ENERGY LANDSCAPES | KINETICS | MUTATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | MOLECULAR-DYNAMICS SIMULATIONS
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 02/2011, Volume 133, Issue 4, pp. 664 - 667
Protein folding is a classic grand challenge that is relevant to numerous human diseases, such as protein misfolding diseases like Alzheimer’s disease. Solving... 
Journal Article
Advances in Experimental Medicine and Biology, ISSN 0065-2598, 2014, Volume 797, pp. 101 - 106
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 11/2017, Volume 13, Issue 11, p. 5496
N-Methyl-d-aspartate (NMDA) receptors, key neuronal receptors playing the central role in learning and memory, are heavily glycosylated in vivo. Astonishingly... 
Proteins | Binding | Coupling (molecular) | Receptors | Computer simulation | Molecular dynamics | Ligands | Glycoproteins | Glycan | Molecular chains
Journal Article
Computing in Science & Engineering, ISSN 1521-9615, 07/2010, Volume 12, Issue 4, pp. 34 - 39
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 03/2015, Volume 142, Issue 12, p. 124105
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 06/2017, Volume 13, Issue 6, p. 2440
Metadynamics is a powerful enhanced molecular dynamics sampling method that accelerates simulations by adding history-dependent multidimensional Gaussians... 
Computer simulation | Independent component analysis | Molecular dynamics | Markov chains | Sampling | Molecular chains
Journal Article
Methods, ISSN 1046-2023, 09/2010, Volume 52, Issue 1, pp. 99 - 105
Journal Article
Nature Communications, ISSN 2041-1723, 03/2014, Volume 5, Issue 1, p. 3397
Journal Article
Nature Communications, ISSN 2041-1723, 11/2016, Volume 7, Issue 1
Journal Article
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
Biophysical Journal, ISSN 0006-3495, 12/2012, Volume 103, Issue 12, pp. L47 - L49
Amyloid beta (A ) peptide plays an important role in Alzheimer’s disease. A number of mutations in the A sequence lead to familial Alzheimer’s disease,... 
Biophysical Letter
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2012, Volume 8, Issue 4, pp. 1409 - 1414
Recent hardware and software advances have enabled simulation studies of protein systems on biophysically relevant time scales, often revealing the need for... 
WATER MODEL | MECHANICS | REPARAMETRIZATION | UBIQUITIN | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | DYNAMICS | ENERGETICS | CHEMISTRY, PHYSICAL | HELIX | SIMULATIONS | BACKBONE | PEPTIDE
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 02/2010, Volume 132, Issue 5, pp. 1526 - 1528
To date, the slowest-folding proteins folded ab initio by all-atom molecular dynamics simulations have had folding times in the range of nanoseconds to... 
TRANSITION | HETEROGENEITY | DYNAMICS | DESIGN | CHEMISTRY, MULTIDISCIPLINARY | KINETICS | Markov Chains | Arabidopsis - chemistry | Transcription Factors - chemistry | Time Factors | Protein Conformation | Molecular Dynamics Simulation | Protein Folding | Molecular dynamics | Usage | Solvation | Chemical reaction, Rate of | Protein folding | Analysis
Journal Article
The Journal of Physical Chemistry Letters, ISSN 1948-7185, 06/2014, Volume 5, Issue 11, pp. 1885 - 1891
The development of accurate molecular mechanics force fields is a significant challenge that must be addressed for the continued success of molecular... 
Molecular Structure, Quantum Chemistry, and General Theory | force field | water model | optimization | TIP4P | TIP3P | water | ForceBalance | MOLECULAR SIMULATION | MATERIALS SCIENCE, MULTIDISCIPLINARY | ALGORITHM | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | LIQUID WATER | CHEMISTRY, PHYSICAL | NANOSCIENCE & NANOTECHNOLOGY | BASIS-SETS | MODEL
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2018, Volume 14, Issue 4, p. 1887
Variational autoencoder frameworks have demonstrated success in reducing complex nonlinear dynamics in molecular simulation to a single nonlinear embedding. In... 
Proteins | Coders | Nonlinear dynamics | Alanine | Computer simulation | Neural networks | Independent component analysis | Linear transformations | Embedding | Sampling | Dynamical systems | Molecular chains
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 01/2014, Volume 136, Issue 2, pp. 528 - 546
Journal Article