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We applied temperature parallel simulated annealing to the biological problem of folding simulation. Water- counting is introduced to formulate folding ...
Oct 23, 2015 · Our simulation with simulated annealing algorithm at high temperatures cannot solve the force-field bias in folding study. The results imply ...
In this paper a Simulated Annealing algorithm (SA) for solving the Protein Folding Problem (PFP) is presented. This algorithm has two phases: quenching and ...
Feb 19, 2024 · The simulated-annealing PLA folding algorithm uses a cost function considering the square of input and output densities, providing a refined ...
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A standard method to enhance conformational sampling uses simulated annealing (SA-MD) that is to start with simulations at high temperature to overcome barriers ...
In this paper, we propose a new hybrid scheme of parallel tempering and simulated annealing (hybrid PT/SA). Within the hybrid PT/SA scheme, ...
Nov 21, 2024 · In this paper a Simulated Annealing algorithm (SA) for solving the Protein Folding Problem (PFP) is presented.
Abstract. Protein folding problem is one of the most important problems in bioinformatics. By combining simulated annealing method with pull moves which is ...
This method employs independent parallel Monte Carlo random walks in several parallel simulations carried out at different temperatures. System states, defined ...
This paper introduces a variant of molecular dynamics-based simulated annealing that is useful for optimizing atomistic structures.