This paper addresses the elementary shortest path problem with forbidden paths. The main aim is to find the shortest paths from a single origin node to every other node of a directed graph, such that the solution does...
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This paper addresses the elementary shortest path problem with forbidden paths. The main aim is to find the shortest paths from a single origin node to every other node of a directed graph, such that the solution does not contain any path belonging to a given set (i.e., the forbidden set). It is imposed that no cycle can be included in the solution. The problem at hand is formulated as a particular instance of the shortest path problem with resource constraints and two different solution approaches are defined and implemented. One is a Branch & Bound based algorithm, the other is a dynamic programming approach. Different versions of the proposed solution strategies are developed and tested on a large set of test problems. (C) 2012 Elsevier B.V. All rights reserved.
In this article, we propose a new extension to a dynamicprogramming Algorithm (DPA) approach for Track-before-Detect challenges. This extension enables the DPA to process time-delayed sensor data directly. Such delay...
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In this article, we propose a new extension to a dynamicprogramming Algorithm (DPA) approach for Track-before-Detect challenges. This extension enables the DPA to process time-delayed sensor data directly. Such delay might appear because of delays in communication networks. The extended DPA is identical to the recursive standard DPA in case of all sensor data appear in the timely correct order. Furthermore, an intense evaluation of the Accumulated State Density (ASD) filter is given on simulation data. Last but not least, we apply a combination of DPA and ASD on data of a real radar system and present the resulting tracks. Our experience concerning this combination is a seamless cooperation between the track initialization by DPA and a track maintenance by ASD filter.
Background: Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the...
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Background: Hydrogen bonds play a major role in the stabilization of protein-ligand complexes. The ability of a functional group to form them depends on the position of its hydrogen atoms. An accurate knowledge of the positions of hydrogen atoms in proteins is therefore important to correctly identify hydrogen bonds and their properties. The high mobility of hydrogen atoms introduces several degrees of freedom: Tautomeric states, where a hydrogen atom alters its binding partner, torsional changes where the position of the hydrogen atom is rotated around the last heavy-atom bond in a residue, and protonation states, where the number of hydrogen atoms at a functional group may change. Also, side-chain flips in glutamine and asparagine and histidine residues, which are common crystallographic ambiguities must be identified before structure-based calculations can be conducted. Results: We have implemented a method to determine the most probable hydrogen atom positions in a given protein-ligand complex. Optimality of hydrogen bond geometries is determined by an empirical scoring function which is used in molecular docking. This allows to evaluate protein-ligand interactions with an established model. Also, our method allows to resolve common crystallographic ambiguities such as as flipped amide groups and histidine residues. To ensure high speed, we make use of a dynamic programming approach. Conclusion: Our results were checked against selected high-resolution structures from an external dataset, for which the positions of the hydrogen atoms have been validated manually. The quality of our results is comparable to that of other programs, with the advantage of being fast enough to be applied on-the-fly for interactive usage or during score evaluation.
In the present paper,we describe how a directed graph was constructed and then searched forthe optimum path using a dynamic programming approach,based on the secondary structure propensity ofthe protein short sequence...
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In the present paper,we describe how a directed graph was constructed and then searched forthe optimum path using a dynamic programming approach,based on the secondary structure propensity ofthe protein short sequence derived from a training data *** protein secondary structure was thus pre-dicted in this *** average three-state accuracy of the algorithm used was 76.70%.
Background: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary prote...
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Background: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain. Results: Distance matrices of various branches of the human kinome, that is the full complement of human kinases, were developed that matched the phylogenetic tree of the human kinome establishing the efficacy of the global alignment of the algorithm. PKCd and PKCe kinases share close biological properties and structural similarities but do not give high scores with character based alignments. Detailed comparison established close similarities between subsequences that do not have any significant character identity. We compared their known 3D structures to establish that the algorithm is able to pick subsequences that are not considered similar by character based matching algorithms but share structural similarities. Similarly many subsequences with low character identity were picked between xyna-theau and xyna-clotm F/10 xylanases. Comparison of 3D structures of the subsequences confirmed the claim of similarity in structure. Conclusion: An algorithm is developed which is inspired by successful application of spectral similarity applied to music sequences. The method captures subsequences that do not align by traditional character based alignment tools but give rise to similar secondary and tertiary structures. The Spectral Similarity Score (SSS) is an ex
Motivation: Prediction of gene structure in newly sequenced DNA becomes very important in large genome sequencing projects. This problem is complicated due to the exon-intron structure of eukaryotic genes and because ...
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Motivation: Prediction of gene structure in newly sequenced DNA becomes very important in large genome sequencing projects. This problem is complicated due to the exon-intron structure of eukaryotic genes and because gene expression is regulated by many different short nucleotide domains. In order to be able to analyse the full gene structure in different organisms, if is necessary to combine information about potential functional signals (promoter region, splice sires, start and stop codons, 3' untranslated region) together with the statistical properties of coding sequences (coding potential), information about homologous proteins, ESTs and repented elements. Results: We have developed the GeneBuilder system which is based on prediction of functional signals and coding regions by different approaches in combination with similarity searches in proteins and EST databases. The potential gene structure models are obtained by using a dynamicprogramming method. The program permits the use of several parameters for gene structure prediction and refinement. During gene model construction, selecting different exon homology, levels with a protein sequence selected from a list of homologous proteins can improve the accuracy of the gene structure prediction. In the case of low homology GeneBuilder is still able to predict the gene structure. The GeneBuilder system has been tested bq, using the standard set (Burset and Guigo, Genomics, 34, 353-367, 1996) and rite performances are: 0.89 sensitivity, and 0.91 specificity at the nucleotide level. The total correlation coefficient is 0.88. Availability: The GeneBuilder system is implemented as a part of the WebGene a rite URL. http://***/webgene and TRADAT(TRAncription Database and Analysis Tools) launcher URL: http://***/tradat. Contact: milanesi@***
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