Structure optimization in an off-lattice protein model
نویسندگان
چکیده
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 all chain lengths ≥ 13. This indicates that PERM has the potential to produce native states also for more realistic protein models. For d = 3, where no published ground states exist, we present some putative lowest energy states for future comparison with other methods.
منابع مشابه
A balance-evolution artificial bee colony algorithm for protein structure optimization based on a three-dimensional AB off-lattice model
Protein structure prediction is a fundamental issue in the field of computational molecular biology. In this paper, the AB off-lattice model is adopted to transform the original protein structure prediction scheme into a numerical optimization problem. We present a balance-evolution artificial bee colony (BE-ABC) algorithm to address the problem, with the aim of finding the structure for a give...
متن کاملA Quasi-physical Algorithm for the Structure Optimization in an Off-lattice Protein Model
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 pruned-enriched-Rosenbluth method (PERM), hitherto employed to native state searches only for off-lattice models. For two dimensions we found states with lower energy than previously proposed putative ground states for ...
متن کاملProtein secondary structure optimization using an improved artificial bee colony algorithm based on AB off-lattice model
Predicting the secondary structure of protein has been the focus of scientific research for decades, but it remains to be a challenge in bioinformatics due to the increasing computation complexity. In this paper, AB off-lattice model is introduced to transforms the prediction task into a numerical optimization problem. Artificial Bee Colony algorithm (ABC) is an effective swarm intelligence alg...
متن کاملCut-off Grade Optimization for Maximizing the Output Rate
In the open-pit mining, one of the first decisions that must be made in production planning stage, after completing the design of final pit limits, is determining of the processing plant cut-off grade. Since this grade has an essential effect on operations, choosing the optimum cut-off grade is of considerable importance. Different goals may be used for determining optimum cut-off grade. One of...
متن کاملAnnealing contour Monte Carlo algorithm for structure optimization in an off-lattice protein model.
We present a space annealing version for a contour Monte Carlo algorithm and show that it can be applied successfully to finding the ground states for an off-lattice protein model. The comparison shows that the algorithm has made a significant improvement over the pruned-enriched-Rosenbluth method and the Metropolis Monte Carlo method in finding the ground states for AB models. For all sequence...
متن کامل