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The edge (vertex) connectivity of a graph is the minimum number of edges (vertices) that must be removed to disconnect the graph. Connectivity is an important property of a graph but has seldom been used in the study of protein-protein interaction (PPI) ...

Modeling protein interaction data with graphs (networks) is insufficient for some common types of experimentally generated interaction data. For example, in affinity purification experiments, one protein is pulled out of the cell along with other ...

The directionality of protein interactions is the prerequisite of forming various signaling networks, and the construction of signaling networks is a critical issue in the discovering the mechanism of the life process. In this paper, we proposed a novel ...

Computational drug repositioning offers promise for discovering new uses of existing drugs, as drug related molecular, chemical, and clinical information has increased over the past decade and become broadly accessible. In this study, we present a new ...

Recently, several domain-based computational models for predicting protein-protein interactions (PPIs) have been proposed. The conventional methods usually infer domain or domain combination (DC) interactions from already known interacting sets of ...

Finding protein complexes and their functions is essential work for understanding biological process. However, one of the difficulties in inferring protein complexes from protein-protein interaction(PPI) network originates from the fact that protein ...

We present a new and faster algorithm for predicting coevolving proteins from pairs of protein distance matrices that are free to differ in size and scale, based on the initial work in [3]. The new algorithm has a more effective pruning strategy for ...

In this work we approach the problem of predicting protein binding hot spot residues through a combination of classifiers. We consider a comprehensive set of structural and chemical properties reported in the literature for characterizing hot spot ...

We study transitivity properties of edge weights in complex networks. We show that enforcing transitivity leads to a transitivity inequality which is equivalent to ultra-metric inequality. This can be used to define transitive closure on weighted ...

Automated information extraction systems from biomedical text have been reported. Some systems are based on manually developed rules or pattern matching. Manually developed rules are specific for analysis, however, new rules must be developed for each ...

Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface ...

There is an emerging trend in post-genome biology to study the collection of thousands of protein interaction pairs (protein interactome) derived from high-throughput experiments. However, high-throughput protein interactome data, especially when ...

Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface ...

TRANSPATH^® can either be used as an encyclopedia, for both specific and general information on signal transduction, or can serve as a network analyser. Therefore, three modules have been created: the first one is the data, which have been manually ...

In recent years, the biomolecular sciences have been driven forward by overwhelming advances in new biotechnological high-throughput experimental methods and bioinformatic genome-wide computational methods. Such breakthroughs are producing huge amounts ...