The problem of multiple sequence alignment is one of the most important problems in computational biology. In this paper we present a new method that simultaneously performs multi...
Jaroslaw Zola, Denis Trystram, Andrei Tchernykh, C...
Background: We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protoco...
To solve real-world discrete optimization problems approximately metaheuristics such as simulated annealing and other local search methods are commonly used. For large instances o...
In this paper we describe a methodology that includes the complementary use of simulated annealing and response surface methodology (RSM). The methodology was developed for analys...
— This paper presents an improvement to the vanilla version of the simulated annealing algorithm by using opposite neighbors. This new technique, is based on the recently propose...