Results 11 to 20 of about 633,406 (289)

Molecular dynamics simulations [PDF]

Current Biology, 1997
Originally the province of theorists only, molecular dynamics simulations are now accessible to a broad range of scientists. Advances in methodology, coupled with the development of fast and relatively inexpensive computer workstations, have increased the efficiency, accuracy, reliability, and applicability of these methods. Crossing important research
openaire   +2 more sources

Phase changes in 38 atom Lennard-Jones clusters. II: A parallel tempering study of equilibrium and dynamic properties in the molecular dynamics and microcanonical [PDF]

, 2000
We study the 38-atom Lennard-Jones cluster with parallel tempering Monte Carlo methods in the microcanonical and molecular dynamics ensembles. A new Monte Carlo algorithm is presented that samples rigorously the molecular dynamics ensemble for a system ...
Calvo, F., Doll, J. D., Freeman, David L., Neirotti, J. P.   +3 more
core   +3 more sources

Molecular Dynamics Simulations of Weak Detonations [PDF]

, 2011
Detonation of a three-dimensional reactive non-isotropic molecular crystal is modeled using molecular dynamics simulations. The detonation process is initiated by an impulse, followed by the creation of a stable fast reactive shock wave.
A. N. Dremin, B. M. Rice, D. C. Sorescu, J. A. Zukas, J. Von Neumann, M. Ben-Artzi, M. P. Allen, Morag Am-Shallem, Ronnie Kosloff, Sergey V. Zybin, V. Balalaev, W. Fickett, Ya. B. Zel'dovich, Ya. B. Zel'dovich, Ya. B. Zel'dovich, Yehuda Zeiri   +15 more
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Computational Studies on the Inhibitor Selectivity of Human JAMM Deubiquitinylases Rpn11 and CSN5

Frontiers in Chemistry, 2018
Deubiquitinylases (DUBs) are highly specialized enzymes which are responsible for removal of covalently attached ubiquitin(s) from the targeted proteins. DUBs play an important role in maintaining the protein homeodynamics. Recently, DUBs have emerged as
Vikash Kumar, Vikash Kumar, Michael Naumann, Matthias Stein   +3 more
doaj   +1 more source

Discrete molecular dynamics simulations of peptide aggregation [PDF]

, 2003
We study the aggregation of peptides using the discrete molecular dynamics simulations. At temperatures above the alpha-helix melting temperature of a single peptide, the model peptides aggregate into a multi-layer parallel beta-sheet structure.
A.T. Petkova, A.V. Smith, A.V. Smith, B. Urbanc, C. Soto, D. Bratko, D.A. Kirschner, E.D. Eanes, F. Chiti, F. Ding, F. Ding, F. Ding, F. Ding, G. Bitan, G. Bitan, H. E. Stanley, H. Taketomi, H.M. Berman, J. Shimada, J.D. Sipe, J.M. Borreguero, J.S. Richardson, L. Bonar, L. Cruz, L.C. Serpell, M. Coles, M. Sunde, N. V. Dokholyan, N.V. Dokholyan, O. Gursky, P.J. Kraulis, R. Jaenicke, S. Peng, S. V. Buldyrev, S.B. Malinchik, Y. Zhou   +35 more
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Crossing the Boundaries within Computational Chemistry: From Molecular Dynamics to Cheminformatics and back

CHIMIA, 2014
The research in the group for computational chemistry at the ETH Zurich focuses on the development of methods and software for classical molecular dynamics simulations and cheminformatics, and their application to biological and chemical ...
Sereina Riniker
doaj   +1 more source

Computational Design of Nanobody Binding to Cortisol to Improve Their Binding Affinity Using Molecular Docking and Molecular Dynamics Simulations

Indonesian Journal of Chemistry, 2022
Currently, nanobody binding cortisol has been deposited in the database. Unfortunately, the affinity is still in micromolar order. Substituting hydrophobic residues in the binding pocket and utilizing CDR2 and CDR3 is the strategy to improve the affinity.
Umi Baroroh, Nur Asni Setiani, Irma Mardiah, Dewi Astriany, Muhammad Yusuf   +4 more
doaj   +1 more source

Molecular Dynamics Simulations of Poly(dimethylsiloxane) Elasticity [PDF]

, 2018
Cross-linked polymers have unique and advantageous properties due to the infinite elastic chains. Poly(dimethylsiloxane) (PDMS) belongs into a group of non-toxic, relatively inert and highly elastic polymers (elastomers).
Jakoubková J., Kalvoda L.
core   +1 more source

Molecular Dynamics Simulations of Drug-Conjugated Cell-Penetrating Peptides

Pharmaceuticals, 2023
Cell-penetrating peptides (CPPs) are small peptides capable of translocating through biological membranes carrying various attached cargo into cells and even into the nucleus. They may also participate in transcellular transport.
Márton Ivánczi, Balázs Balogh, Loretta Kis, István Mándity   +3 more
doaj   +1 more source

Molecular dynamics simulations and drug discovery

BMC Biology, 2011
This review discusses the many roles atomistic computer simulations of macromolecular (for example, protein) receptors and their associated small-molecule ligands can play in drug discovery, including the identification of cryptic or allosteric binding ...
Durrant Jacob D, McCammon J Andrew
doaj   +1 more source