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STRIKE was introduced and implemented to predict protein-protein interactions where proteins interact if they contain similar substrings of amino acids. On the yeast protein interaction literature, STRIKE was shown to improve upon the existing state-of-the-art methods for protein-protein interaction prediction. Herein, we describe the parallelization of STRIKE and its multithreaded implementation...
This paper presents a novel approach for solving the Multiple Sequence Alignment (MSA) problem. K-Means clustering is combined with the Rubber Band Technique (RBT) to introduce an iterative optimization algorithm, namely RBT-Km, to find the optimal alignment for a set of input protein sequences. In this technique, the MSA problem is modeled as a Rubber Band, while the solution space is modeled as...
Tabu Search (TS) algorithm is one of optimization search methods and has been applied for a large number of combinatorial optimization problems. In the paper, an improved TS algorithm is proposed for protein 3D folding structure prediction in off-lattice AB model. Experimental results show that the lowest energies computed by the improved TS algorithm are better than those obtained by the previous...
Graphs are frequently used to describe the geometry and also the physicochemical composition of protein active sites. Here, the concept of graph alignment as a novel method for the structural analysis of protein binding pockets is presented. Using inexact graph-matching techniques, one is able to identify both conserved areas and regions of difference among different binding pockets. Thus, using multiple...
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