MOTIVATION Much research has been devoted to the characterization of interaction interfaces found in complexes with known structure. In this context, the interactions of non-homologous domains at equivalent binding sites are of particular interest, as they can reveal convergently evolved interface motifs. Such motifs are an important source of information to formulate rules for interaction spec...

A simple method for predicting residues involved in protein interaction sites is proposed. In the absence of any structural report, the procedure identifies linear stretches of sequences as "receptor-binding domains" (RBDs) by analysing hydrophobicity distribution. The sequences of two databases of non-homologous interaction sites eliciting various biological activities were tested; 59-80 % wer...

Protein-protein interactions are facilitated by a myriad of residue-residue contacts on the interacting proteins. Identifying the site of interaction in the protein is a key for deciphering its functional mechanisms, and is crucial for drug development. Many studies indicate that the compositions of contacting residues are unique. Here, we describe a neural network that identifies protein-prote...

The binding of the "activated" receptor-glucocorticoid complexes of cultured rat hepatoma cells to nuclei, chromatin, and DNA has been studied under cell-free conditions. A critical factor in determining the shape of the binding curve is shown to be an inhibitory material which is present in crude cytosol and which can be removed without destroying the receptor-steroid complex. These and other ...

Protein-protein interactions play a crucial role in many biological processes such as immune response, enzyme catalysis, and signal transduction. Identifying the interacting sites between the proteins is important for understanding the functional mechanisms, and is crucial for drug development. Interaction profile hidden Markov model (ipHMM) was shown to be an effective tool for modeling protei...