Two Perturbations for Geometry Optimization of Off-lattice Bead Protein Models
نویسندگان
چکیده
منابع مشابه
Folding Properties in Off-Lattice Protein Models
The thermodynamic behavior of an oo-lattice model for protein folding is probed in two and three dimensions. The model has only two types of residues, hydrophobic and hydrophilic. Our ability to map out the thermodynamics of the oo-lattice models relies heavily upon the eeciency of the simulated tempering algorithm. In this approach, the temperature is a uctuating variable, enabling the crossin...
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The global structural optimization is carried out for off-lattice protein AB models in two and three dimensions by conformational space annealing. The models consist of hydrophobic and hydrophilic monomers in Fibonacci sequences. To accelerate the convergence, we have introduced a shift operator in the internal coordinate system, and effectively reduced the search space by forming a quotient sp...
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Off-lattice proteinlike models are constructed in two dimensions so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are determined with a high degree of certainty through Monte Carlo processes. The sequences are characterized thermodynamically and kinetically. It is shown that ...
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Model off-lattice sequences in two dimensions are constructed so that their native states are close to an on-lattice target. The Hamiltonian involves the Lennard-Jones and harmonic interactions. The native states of these sequences are determined with a high degree of certainty through Monte Carlo processes. The sequences are characterized thermodynamically and kinetically. It is shown that the...
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We study an off-lattice protein toy model with two species of monomers interacting through modified Lennard-Jones interactions. Low energy configurations are optimized using the prunedenriched-Rosenbluth method (PERM), hitherto employed to native state searches only for off lattice models. For 2 dimensions we found states with lower energy than previously proposed putative ground states, for al...
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ژورنال
عنوان ژورنال: Molecular Informatics
سال: 2017
ISSN: 1868-1743
DOI: 10.1002/minf.201600096