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This paper refines and introduces a modification to the Marriage in Honey Bee Optimisation algorithm (MBO). The modified algorithm was applied to predict the structure of Met-enkphaline using torsion angles representation and ECEPP/3 energy function. The results showed the significance of the modification. The algorithm was able to find the lowest reported free energy conformation of value -12.43...
In this paper, we present a means to fold amino acid interaction networks. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Our approach consists in exploiting the parallel between topological and structural properties. Thus, we establish a relation between the sequence and the structure relying on topological criteria. To fold this type...
Existing studies on graph mining focus on exact graphs that are precise and complete. However, graph data tends to be uncertain in practice due to noise, incompleteness and inaccuracy. This paper investigates the problem of finding top-k maximal cliques in an uncertain graph. A new model of uncertain graphs is presented, and an intuitive measure is introduced to evaluate the significance of vertex...
Ribonucleic acid (RNA) has important structural and functional roles in the cell and plays roles in many stages of protein synthesis. The structure of RNA largely determines its function. Current physical methods for structure determination are time-consuming and expensive, thus the methods for the computational prediction of structure are necessary. Various algorithms that have been used for RNA...
This article presents a comprehensive study on the main characteristics of a novel optimization algorithm specifically designed for simulation of protein-ligand interactions. Though design of optimization algorithms has been a research issue extensively studied by computer scientists for decades, the emerging applications in bioinformatics such as simulation of protein-ligand interactions and protein...
Proteins are essential for the biological processes in the human body. They can only perform their functions when they fold into their tertiary structure. Protein structure can be determined experimentally and computationally. Experimental methods are time consuming and high-priced and it is not always feasible to identify the protein structure experimentally. In order to predict the protein structure...
Tabu search is a meta-heuristic approach that is found to be useful in solving combinatorial optimization problems. This paper employs the adaptive memory features of tabu search to deal with protein folding problem. A kind of optimization of the neighborhood scale is presented, where a annealing mechanism is also used to enhance the searching ability for optimum solutions of the AB off-lattice model...
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