In the protein sequence space, natural proteins form clusters of families which are characterized by their unique native folds whereas the great majority of random polypeptides are neither clustered nor foldable to unique structures. Since a given polypeptide can be either foldable or unfoldable, a kind of "folding transition" is expected at the boundary of a protein family in the sequence spac...

Background: The hyaluronidases are the enzymes hydrolyze β-1, 4 glycosidic linkage of hyaluronan. Hyaluronan is a polymer consisting of a repeating disaccharide unit found in cumulus ovuforus complex, semen liquid and other tissue. Addition to hydrolyzing the hyaluronan, hyaluronidase can penetrate through the cumulus cells layer that surrounds the oocyte, thus it terms spreading factor. Moreov...

We have designed, trained and tested two types of neural networks for the prediction of protein folding pattern from sequence. Here we describe the differences in the networks and compare their performance on a variety of proteins. Both network representations are generally successful in predicting protein fold and can also be used together to confirm a prediction.

The pattern matching is a well known and important task of the pattern discovery process in today’s world for finding the nucleotide or amino acid sequence patterns in protein sequence databases. Although pattern matching is commonly used in computer science, its applications cover a wide range, including in editors, information retrieval. In this paper we propose a new pattern matching algorit...

The MIPS group (Martinsried Institute for Protein Sequences) at the Max-Planck-Institute for Biochemistry, Martinsried near Munich, Germany, collects, processes and distributes protein sequence data within the framework of the tripartite association of the PIR-International Protein Sequence Database (,). MIPS contributes nearly 50% of the data input to the PIR-International Protein Sequence Dat...

Mg+2/Mn+2-dependent type 2C protein phosphatases (PP2Cs) are ubiquitous in eukaryotes, mediating diverse cellular signaling processes through metal ion catalyzed dephosphorylation of target proteins. We have identified a distinct PP2C sequence class ("PP2C7s") which is nearly universally distributed in Eukaryotes, and therefore apparently ancient. PP2C7s are by far most prominent and diverse in...