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Journal of Molecular Biology, ISSN 0022-2836, 05/2007, Volume 368, Issue 5, pp. 1448 - 1457
The role of peptides Aβ40 and Aβ42 in the early pathogenesis of Alzheimer's disease (AD) is frequently emphasized in the literature. It is known that Aβ42 is... 
amyloid-β peptides | conformational ensemble | Alzheimer's disease | J-coupling constants | replica exchange molecular dynamics
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 02/2013, Volume 9, Issue 2, pp. 1282 - 1293
Accurate and reliable calculation of protein-ligand binding affinities remains a hotbed of computer-aided drug design research. Despite the potentially large... 
CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE | ACCURATE | LIGAND-BINDING | PROTEIN | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
Journal Article
International Journal of Biochemistry and Cell Biology, ISSN 1357-2725, 06/2018, Volume 99, pp. 19 - 27
Alzheimer’s disease is a severe brain illness that causes vast numbers of nerve cells in the brain to die, driven by the production and deposition of amyloid... 
Intrinsically disordered protein | Alzheimer’s disease | Osmolytes | Replica exchange molecular dynamics
Journal Article
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 12/2013, Volume 9, Issue 12, pp. 5430 - 5449
Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and... 
INITIO QUANTUM-CHEMISTRY | COLD-SHOCK PROTEIN | FLUCTUATING CHARGE | LIGAND-BINDING | N-15 NMR RELAXATION | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE METHOD | POTENTIAL FUNCTIONS | PANCREATIC TRYPSIN-INHIBITOR | MOLECULAR-DYNAMICS SIMULATIONS | BETA-HAIRPIN FORMATION
Journal Article
Journal of Medicinal Chemistry, ISSN 0022-2623, 05/2016, Volume 59, Issue 9, pp. 4035 - 4061
Journal Article
Journal of the American Chemical Society, ISSN 0002-7863, 07/2018, Volume 140, Issue 27, pp. 8479 - 8486
Cataracts are a leading cause of vision impairment, which stem from the misfolding and aggregation of crystallins in the eye lens. Despite its prevalence and... 
MUTANT | PROTEIN | STABILITY | REPLICA-EXCHANGE | CHEMISTRY, MULTIDISCIPLINARY | ALPHA-CRYSTALLIN | CATARACT
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 05/2007, Volume 126, Issue 18, pp. 184110 - 184110-10
The authors present a method to calculate free energy differences between two states A and B "on the fly" from a single molecular dynamics simulation of a... 
REPLICA-EXCHANGE METHOD | MOLECULAR-DYNAMICS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
Journal Article
Journal of Physical Chemistry B, ISSN 1520-6106, 09/2018, Volume 122, Issue 37, pp. 8698 - 8705
Peptides are promising drug candidates with advantageous therapeutic properties. However, their inherent flexibility makes the development of... 
PEPTIDES | PARAMETERIZATION | ORIENTATION | ENVIRONMENT | DYNAMICS | MEMBRANES | IMPLEMENTATION | CHEMISTRY, PHYSICAL | REPLICA-EXCHANGE | FORCE-FIELDS | WATER
Journal Article
Wiley Interdisciplinary Reviews: Computational Molecular Science, ISSN 1759-0876, 09/2011, Volume 1, Issue 5, pp. 826 - 843
Metadynamics is a powerful technique for enhancing sampling in molecular dynamics simulations and reconstructing the free‐energy surface as a function of few... 
CONFORMATIONAL-CHANGES | WELL-TEMPERED METADYNAMICS | FREE-ENERGY LANDSCAPE | MATHEMATICAL & COMPUTATIONAL BIOLOGY | REPLICA-EXCHANGE | ATOMISTIC SIMULATIONS | HIV-1 PROTEASE | MOLECULAR-DYNAMICS SIMULATIONS | DEHYDROXYLATION REACTION | CARBON-DIOXIDE | CHEMISTRY, MULTIDISCIPLINARY | AB-INITIO METADYNAMICS
Journal Article
Journal of Physical Chemistry C, ISSN 1932-7447, 12/2011, Volume 115, Issue 47, pp. 23323 - 23328
The adsorption of protein villin headpiece (HP35) onto a graphene has been investigated using large scale molecular dynamics simulations, and the results are... 
MOLECULAR-DYNAMICS | PROTEIN | AROMATIC CONTENT | MATERIALS SCIENCE, MULTIDISCIPLINARY | CHEMISTRY, PHYSICAL | NANOSCIENCE & NANOTECHNOLOGY | REPLICA EXCHANGE | SIMULATION | DEWETTING TRANSITION | PEPTIDES | IN-VIVO | ATOMIC-LEVEL | WATER CHANNEL
Journal Article
Chemical Physics Letters, ISSN 0009-2614, 03/2018, Volume 696, pp. 55 - 60
An extensive replica exchange molecular dynamics (REMD) simulation was performed to investigate the progress patterns of the molecular interactions of... 
Propafenone | Amyloid beta Aβ16-22 | Conformational equilibrium | Replica exchange molecular dynamics | Amyloid beta Aβ
Journal Article
Computer Physics Communications, ISSN 0010-4655, 2009, Volume 180, Issue 10, pp. 1961 - 1972
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most... 
Proteins | Molecular dynamics | Metadynamics | Umbrella sampling | Free energy | BETA-HAIRPIN | MECHANISM | ALGORITHMS | SIMULATION | PHYSICS, MATHEMATICAL | COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS | REPLICA-EXCHANGE | FORCE-FIELD | SYSTEMS | EFFICIENT | Chemical properties | Universities and colleges
Journal Article
ChemPhysChem, ISSN 1439-4235, 07/2019, Volume 20, Issue 13, pp. 1661 - 1661
The Front Cover the structure of a cyclic tetrapeptide in solution. The dynamics of the peptide in explicit solvent was investigated using several... 
cyclic peptides | Replica Exchange Molecular Dynamics | NMR spectroscopy | Quantum Mechanics/Molecular Mechanics | IR spectroscopy
Journal Article