Silvio C. E. Tosatto

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MOTIVATION Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the existence of different disorder flavors. While efficient predictions are required to annotate entire genomes, most existing methods require sequence profiles for disorder prediction, making them cumbersome(More)
Scoring functions are widely used in the final step of model selection in protein structure prediction. This is of interest both for comparative modeling targets, where it is important to select the best model among a set of many good, "correct" ones, as well as for other (fold recognition or novel fold) targets, where the set may contain many incorrect(More)
MOTIVATION Repeat proteins form a distinct class of structures where folding is greatly simplified. Several classes have been defined, with solenoid repeats of periodicity between ca. 5 and 40 being the most challenging to detect. Such proteins evolve quickly and their periodicity may be rapidly hidden at sequence level. From a structural point of view,(More)
MOTIVATION Disordered protein regions are key to the function of numerous processes within an organism and to the determination of a protein's biological role. The most common source for protein disorder annotations, DisProt, covers only a fraction of the available sequences. Alternatively, the Protein Data Bank (PDB) has been mined for missing residues in(More)
MobiDB (http://mobidb.bio.unipd.it/) is a database of intrinsically disordered and mobile proteins. Intrinsically disordered regions are key for the function of numerous proteins. Here we provide a new version of MobiDB, a centralized source aimed at providing the most complete picture on different flavors of disorder in protein structures covering all(More)
MOTIVATION Residue interaction networks (RINs) have been used in the literature to describe the protein 3D structure as a graph where nodes represent residues and edges physico-chemical interactions, e.g. hydrogen bonds or van-der-Waals contacts. Topological network parameters can be calculated over RINs and have been correlated with various aspects of(More)
SUMMARY We present a web server that computes alignments of protein secondary structures. The server supports both performing pairwise alignments and searching a secondary structure against a library of domain folds. It can calculate global and local secondary structure element alignments. A combination of local and global alignment steps can be used to(More)
UNLABELLED The application of novel experimental techniques has generated large networks of protein-protein interactions. Frequently, important information on the structure and cellular function of protein-protein interactions can be gained from the domains of interacting proteins. We have designed a Cytoscape plugin that decomposes interacting proteins(More)
Identifying protein functions can be useful for numerous applications in biology. The prediction of gene ontology (GO) functional terms from sequence remains however a challenging task, as shown by the recent CAFA experiments. Here we present INGA, a web server developed to predict protein function from a combination of three orthogonal approaches. Sequence(More)
MOTIVATION Electrostatic calculations are an important tool for deciphering many functional mechanisms in proteins. Generalized Born (GB) models offer a fast and convenient computational approximation over other implicit solvent-based electrostatic models. Here we present a novel GB-based web server, using the program Bluues, to calculate numerous(More)