BioDec is a SME specialized in bioinformatics, with special emphasis on protein sequence analysis and "knowledge management" software. It originates from a merger between a spin-off of an academic research group and of Information Technology professionals. The mission of the company is to provide high quality products and services for bioinformatics.
BioDec main products are integrated tools (BioDecoding Machines) for decoding and annotating information from biological sequences, with special emphasis on trans-membrane protein detection and classification. When applicable, BIO builds its products as web-based application servers, in order to ease the fruition of the tools by non-specialized users. BIO also strives to use technological standards and state-of-the-art algorithms, and takes advantages of continuous interactions with a world-class academic research group in bioinformatics in the University of Bologna.
Among the products developed by BioDec (for the complete list, http://www.biodec.com/products), the following are the most relevant to the project:
ZenDock- A predictor of the most probable protein-protein interaction sites on a protein surface, that, for every amino acid on the protein surface, allows its classification as an interaction candidate or not, and estimate the prediction reliability.
Tangram- A Fold recognition system. Tangram fold recognition code detects the sequence remote homologi, based on profile-profile alignments validated through entropy-filtering, as described in our Proteins paper [Proteins 54 (2004) 351-360]. The detected remote homology is suitable as templates for model building or for functional annotation of the target sequence.

Ivan Rossi

Dr. Ivan Rossi is president of BioDec and Ph.D. in Computational Chemistry. He is also an adjunct Professor of Computational Biology at the University of Bologna (Italy). Ivan Rossi has fifteen-year experience in applied Computational Chemistry research and eight-year experience in Computational Biology research and development. He is a peer-reviewer for the "Journal of the American Chemical Society" and "Bioinformatics" journals.

Relevant publications/patents

• Fariselli P., Finelli M., Rossi I., Amico M., Zauli A., Martelli P. L., Casadio R.: “TRAMPLE: the transmembrane protein labelling environment" Nucl. Acids Res. 33: W198-W201, (2005).
• Capriotti E., Fariselli P., Rossi I., Casadio R.: "A Shannon Entropy-based filter detects high-quality profile-profile alignments in searches for remote homologues" Proteins 54: 351-360, (2004).
• Fariselli P., Finelli M., Marchignoli D., Martelli P. L., Rossi I., Casadio R.: "MaxSubSeq: an algorithm for segment-length optimisation. The case study of transmembrane-spanning segments" Bioinformatics 19: 500-505, (2003).
• Fariselli P., Zauli A., Rossi I., Finelli M., Martelli P.L., Casadio R.: "A neural network method to improve prediction of protein-protein interaction sites in heterocomplexes" Proceedings of the IEEE International Workshop on Neural Network on Signal Processing 2003, Toulouse (FR), IEEE Press, 33-41, (2003).
• Facchiano A., Facchiano F., Rossi I., Casadio R. "RGD-analog non-peptidic molecules having anti-adhesive, anti-migration anti-proliferative effects" Patent n. WO 02/066421 A1, Patent n. US 2002/0119932 A1
  

Contact:

Dr. Ivan Rossi
BioDec srl
Tel.: +39 051 0548263
Fax: +39 051 7459582
E-Mail: ivan at biodec.com
Website: www.biodec.com