MOTIVATION Protein-protein interactions (PPIs) are a promising, but challenging target for pharmaceutical intervention. One approach for addressing these difficult targets is the rational design of small-molecule inhibitors that mimic the chemical and physical properties of small clusters of key residues at the protein-protein interface. The identification of appropriate clusters of interface r...

The study of protein-protein interactions (PPIs) can be very important for the understanding of biological cellular functions. However, detecting PPIs in the laboratories are both time-consuming and expensive. For this reason, there has been much recent effort to develop techniques for computational prediction of PPIs as this can complement laboratory procedures and provide an inexpensive way o...

Most of the information about protein-protein interactions (PPIs) can only be found in unstructured natural language texts (Ono et al., 2001). PubMed, a publicly accessible database for biomedical literature, nowadays consists of over 20 million citations and is still growing fast. Thus, methods that extract PPIs automatically are of great importance. The extraction of PPIs requires the recogni...

Predicting protein-protein interactions (PPIs) is a challenging task and essential to construct the protein interaction networks, which is important for facilitating our understanding of the mechanisms of biological systems. Although a number of high-throughput technologies have been proposed to predict PPIs, there are unavoidable shortcomings, including high cost, time intensity, and inherentl...

There has been much recent interest in the extraction of PPIs (protein-protein interactions) from biomedical texts, but in order to assist with curation efforts, the PPIs must be enriched with further information of biological interest. This paper describes the implementation of a system to extract and enrich PPIs, developed and tested using an annotated corpus of biomedical texts, and employin...

Recently, we applied structural systems biology to host-pathogen interaction and constructed the human-virus structural interaction network (SIN) based on a combination of solved structures and homology models. Subsequent analysis of the human-virus SIN revealed significant differences between antagonistic human-virus and cooperative within-human protein-protein interactions (PPIs). Although th...

Post-translational protein modifications, such as tyrosine phosphorylation, regulate protein-protein interactions (PPIs) critical for signal processing and cellular phenotypes. We extended an established yeast two-hybrid system employing human protein kinases for the analyses of phospho-tyrosine (pY)-dependent PPIs in a direct experimental, large-scale approach. We identified 292 mostly novel p...

Protein-protein interactions (PPI) are vital processes in molecular biology. However, the current understanding of PPIs is far from satisfactory. Improved methods of predicting PPIs are very much needed. Since experimental methods are labour and time consuming and lack accuracy, the improvement is expected to come from the area of computational methods. We designed and implemented a new algorit...

BACKGROUND Protein-protein interactions (PPIs) are challenging but attractive targets for small chemical drugs. Whole PPIs, called the 'interactome', have been emerged in several organisms, including human, based on the recent development of high-throughput screening (HTS) technologies. Individual PPIs have been targeted by small drug-like chemicals (SDCs), however, interactome data have not be...

Anthrax toxin comprises three different proteins, jointly acting to exert toxic activity: a non-toxic protective agent (PA), toxic edema factor (EF), and lethal factor (LF). Binding of PA to anthrax receptors promotes oligomerization of PA, binding of EF and LF, and then endocytosis of the complex. Homomeric forms of PA, complexes of PA bound to LF and to the endogenous receptor capillary morph...