Protein-protein interactions are fundamental as many proteins mediate their biological function through protein interactions. Over the past 20 years there have been many computational approaches to dock proteins. These approaches are mostly based on the shape complementarity of structures and the physio-chemical properties ...

Flux estimation by using isotopomer information of metabolites is currently the only method that can give quantitative estimates of the activity of metabolic pathways. However, the measurement of isotopomer distributions of intermediate metabolites is costly and tedious with current technologies. In this paper we study ...

We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA ...

Amino acid changing mutations in proteins are contstrained by purifying selection and accumulate at different rates. We estimate evolutionary rates on multiple alignments of eukaryotic protein families in a maximum likelihood framework. We find that the evolution of indispensable proteins is constrained by selection and ...

In most studies concerning expression data analyses information on the variability of gene intensity across samples is usually exploited. This information is sensitive to initial data processing which affects the final conclusions. However expression data contains scale free information which is directly comparable between ...

With increasing number of pathways available in public databases, the process of inferring gene regulatory networks becomes more and more feasible. The major problem of most of these pathways is that they are very often faulty or describe only parts of a regulatory system due to limitations of the experimental techniques ...

Functional annotation of unknown proteins is a major goal in proteomics. A key step in this annotation process is the definition of a protein's subcellular localization. As a consequence, numerous prediction techniques for localization have been developed over the years. These methods typically focus on a single underlying ...