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Molecular Dynamics Simulations [PDF]
, 2008 Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that ...
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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
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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 +3 more
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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
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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 +4 more
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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.
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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 +3 more
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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
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Frontiers in Chemistry, 2021 Glutamine 5′-phosphoribosylpyrophosphate amidotransferase (GPATase) catalyzes the synthesis of phosphoribosylamine, pyrophosphate, and glutamate from phosphoribosylpyrophosphate, as well as glutamine at two sites (i.e., glutaminase and ...
Congcong Li +7 more
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Nonequilibrium Molecular Dynamics Simulations of Coal Ash
Energies, 2020 Both molecular dynamics (MD) and nonequilibrium molecular dynamics (NEMD) simulations were performed to simulate coal ashes using the Guillot-Sator model in this work.
Shi Yu +4 more
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