منابع مشابه
Improving an all-atom force field.
Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve...
متن کاملProtein model refinement using an optimized physics-based all-atom force field.
One of the greatest challenges in protein structure prediction is the refinement of low-resolution predicted models to high-resolution structures that are close to the native state. Although contemporary structure prediction methods can assemble the correct topology for a large fraction of protein domains, such approximate models are often not of the resolution required for many important appli...
متن کاملProtein simulations combining an all-atom force field with a Go term
Using a variant of parallel tempering, we study the changes in sampling within a simulation when the all-atom model is coupled to a Go-like potential. We find that the native structure is not the lowest-energy configuration in the all-atom force field. Adding a Go-term deforms the energy landscape in a way that the native configuration becomes the global minimum.
متن کاملNew all-atom force field for molecular dynamics simulation of an AlPO4-34 molecular sieve
A force field of the triclinic framework of AlPO(4)-34, important in methanol-hydrocarbon conversion reactions, was developed using an empirical potential function. Molecular dynamics simulation of an AlPO(4)-34 triclinic framework segment of 1216 atoms, containing the template molecules isopropylamine and water, was performed with explicit consideration of atomic charges. The average RMS diffe...
متن کاملAn all atom force field for simulations of proteins and nucleic acids.
We present an all atom potential energy function for the simulation of proteins and nucleic acids. This work is an extension of the CH united atom function recently presented by S. J. Weiner et al. (J . Amer. Chem. SOC., 106,765 (1984). The parameters of our function are based on calculations on ethane, propane, n-butane, dimethyl ether, methyl ethyl ether, tetrahydrofuran, imidazole, indole, d...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Physical Review E
سال: 2007
ISSN: 1539-3755,1550-2376
DOI: 10.1103/physreve.76.012901