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1. Brannetti B, Montecchi-Palazzi L, Zanzoni A, Cesareni G, Helmer-Citterich M iSPOT: a web-based tool for the analysis and recognition of protein domain specificity Meeting: BIOCOMP 2001 - Year: 2001 Full text in a new tab Topic: Abstract: Missing |
2. Brannetti B, Via A, Montecchi-Palazzi L, Cesareni G, Helmer-Citterich M SH3-SPOT: predizione sulla specificita' di riconoscimento dei domini SH3 Meeting: BIOCOMP 2000 - Year: 2000 Full text in a new tab Topic: Abstract: Abbiamo utilizzato SH3-SPOT per effettuare predizioni tra singole sequenze di SH3 e liste di peptidi, proteine o database di proteine (nrl_3d e swissprot). Le predizioni sono in buon accordo con i dati sperimentali ove questi siano disponibili. Il metodo puo' essere utilizzato per predire la specificita' di qualunque proteina di cui siano disponibili: 1) la struttura di almeno un complesso proteina/peptide o proteina/proteina; 2) dati sperimentali di interazione tra proteina e liste di peptidi. Nel caso del dominio SH3, abbiamo attualmente a disposizione 8 strutture di complessi e circa 300 peptidi che si legano ad una ventina di domini SH3. Il potere predittivo del metodo potrebbe aumentare col crescere del database delle strutture o dei dati di phage display. Stiamo attualmente migliorando il programma con il calcolo dell'entropia per "pesare" i residui dell'interfaccia e con la valutazione della lunghezza delle catene laterali dei residui coinvolti nell'interazione nel calcolo della frequenza dei contatti residuo-residuo.Il nuovo programma SPOT verra' applicato all'analisi della specificita' delle molecole MHC e allo studio dell'interazione DNA-proteine. Barbara Brannetti, Allegra Via, Gianluca Cestra, Gianni Cesareni e Manuela Helmer Citterich (2000). SH3-SPOT: an algorithm to predict preferred ligands of different members of the SH3 gene family. JMB in press. |
3. Ceol A, Montecchi-Palazzi L, Persico M, Gavrila C, Castagnoli L, Cesareni G The (new) MINT Database. Meeting: BITS 2004 - Year: 2004 Full text in a new tab Topic: Unspecified Abstract: Scientists recognize that a complete description of cell physiology requires an understanding of the “global” protein interaction network. Thus, a database that collects this information, which is presently dispersed in the scientific literature (or accumulated by high throughput experiments), is an essential post genomic tool. MINT was conceived a couple of years ago, as a collaborative effort between the group of Molecular Genetics and the students of the PhD program of Molecular and Cellular Biology of the University of Rome Tor Vergata, MINT is a relational database designed to store data on functional interactions between proteins, and aims at being exhaustive in the description of the interaction including information, whenever available, about kinetic and binding constants and about the domains participating in the interaction. Presently MINT focuses on experimentally verified interactions extracted from the scientific literature by curators, with special emphasis on mammalian organisms. The MINT protein interaction database offers to the scientific community, a unique bioinformatic tool to design and interpret their experiments. |
4. Cesareni G, Ceol A, Gavrila C, Montecchi-Palazzi L, Persico M, Schneider MV Comparative Interactomics Meeting: BITS 2005 - Year: 2005 Full text in a new tab Topic: Database annotation and data mining Abstract: Motivation:Similar to what has been achieved by comparing genome structures and protein sequences, we hope to obtain valuable information about systems evolution by comparing the organization of interaction networks stored in protein interaction databases and by analyzing their variation and conservation. Equally significantly we can learn whether and how to extend the network information obtained experimentally in well-characterized model systems to different organisms. |
5. Montecchi-Palazzi L, Cabibbo A, Zanzoni A, Helmer-Citterich M, Cesareni G MINT a Molecular INTeraction database Meeting: BIOCOMP 2003 - Year: 2003 Full text in a new tab Topic: Databases: ontologies and integration Abstract: Missing |
6. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G MINT: a Molecular INTeraction database Meeting: BIOCOMP 2002 - Year: 2002 Full text in a new tab Topic: Abstract: Missing |