3 research outputs found
Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics
We describe a combination of all-atom simulations with CABS, a
well-established coarse-grained protein modeling tool, into a single multiscale
protocol. The simulation method has been tested on the C-terminal beta hairpin
of protein G, a model system of protein folding. After reconstructing atomistic
details, conformations derived from the CABS simulation were subjected to
replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb
force fields in explicit solvent. Such a combination accelerates system
convergence several times in comparison with all-atom simulations starting from
the extended chain conformation, demonstrated by the analysis of melting
curves, the number of native-like conformations as a function of time and
secondary structure propagation. The results strongly suggest that the proposed
multiscale method could be an efficient and accurate tool for high-resolution
studies of protein folding dynamics in larger systems.Comment: 12 pages, 4 figure
Modelowanie oddzia艂ywa艅 bia艂ek i peptyd贸w w zredukowanej przestrzeni konformacyjnej.
Celem pracy by艂o opracowanie metody do modelowania oddzia艂ywa艅 bia艂ek i peptyd贸w. Metod臋 oparto na modelu CABS s艂u偶膮cym do modelowania dynamiki pojedynczych 艂a艅cuch贸w bia艂kowych. Poza g艂贸wnym programem opracowano szereg narz臋dzi i po艂膮czono w automatyczn膮 procedur臋 CABSDock. Praca zawiera opis opracowanych narz臋dzi, oraz szereg przyk艂ad贸w zastosowania CABSDock