B - 22 CHARMM - Molecular Dynamics Collaborators
نویسندگان
چکیده
To do its job, whatever it may be among the thousands of life-sustaining jobs proteins do, this dangly chain forged from hundreds of amino acids must fold into just the right threedimensional configuration. It happens within seconds, a long time in protein biochemistry, and the result is a complex bundle of twists and turns with clefts and notches precisely sculpted to allow the protein to attach and release other molecules. Function follows form, and when the form is right, the protein goes to work.
منابع مشابه
Molecular Dynamics Simulation of Water Transportation through Aquaporin-4 in Rat Brain Cells
This paper investigates the mechanism of water transportation through aquaporin-4(AQP4) of ratbrain cells by means of molecular dynamics simulation with CHARMM software. The AQP4 wasembedded into a bilayer made of Dimystroilphosphatylcholine (DMPC). The results illustrate thatwater molecules move through AQP4's channel with change of orientation of oxygen of eachwater molecule.
متن کاملNew faster CHARMM molecular dynamics engine
We introduce a new faster molecular dynamics (MD) engine into the CHARMM software package. The new MD engine is faster both in serial (i.e., single CPU core) and parallel execution. Serial performance is approximately two times higher than in the previous version of CHARMM. The newly programmed parallelization method allows the MD engine to parallelize up to hundreds of CPU cores.
متن کاملMolecular dynamics simulation of interaction of Melittin and DMPC bilayer: Temperature dependence
The interaction between proteins and membranes has an important role in biological pro-cesses.We have calculated energies of interaction between Melittin and DMPC bilayer in differenttemperatures. We have used the CHARMM software for MD simulation under the canonical (N,V, E) ensemble at different temperatures. The computations have shown that water moleculeshave more penetration into the bilay...
متن کاملConformational states of melittin at a bilayer interface.
The distribution of peptide conformations in the membrane interface is central to partitioning energetics. Molecular-dynamics simulations enable characterization of in-membrane structural dynamics. Here, we describe melittin partitioning into dioleoylphosphatidylcholine lipids using CHARMM and OPLS force fields. Although the OPLS simulation failed to reproduce experimental results, the CHARMM s...
متن کاملExplicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
An explicit ion, implicit water solvent model for molecular dynamics was developed and tested with DNA and RNA simulations. The implicit water model uses the finite difference Poisson (FDP) model with the smooth permittivity method implemented in the OpenEye ZAP libraries. Explicit counter-ions, co-ions, and nucleic acid were treated with a Langevin dynamics molecular dynamics algorithm. Ion el...
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تاریخ انتشار 2007