ToolsWe have developed a number of tools that you might find useful:
ESTRELLA designed to characterize mutually exclusive interactors
http://bl210.caspur.it/ESTRELLA/home.php
Sánchez Claros, C. and Tramontano, A. Detecting mutually exclusive interactions in protein-protein interaction maps. submitted
MODalign: A tool to display, evaluate and edit alignments for comparative modeling
http://modorama.biocomputing.
Barbato A., Benkert P., Schwede T., Tramontano A. and Kosinski J. "Improving your target-template alignment with MODalign" (2012) Bioinformatics 28(7):1038-9
MoDiPath: a comprehensive and freely accessible resource collecting linear motifs involved in signaling and metabolic pathways in several organisms.
http://www.biocomputing.it/modipath/
Sayadi A, Briganti L, Tramontano A, Via A (2011) Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs. PLoS One. 2011;6(7):e22270.
DIGIT: a database of immunoglobulin variable domain sequences annotated with the type of antigen, the germline sequences and pairing information between light and heavy chains. User submitted sequences can be blasted against the data base and annotated with the Kabat-Chothia numbering scheme, the location and canonical structures of the CDRs and the mutations with respect to the germline. A 3D model can also be obtained via our 3D modeling tool for immunoglobulin variable domains (PIGS).
http://www.biocomputing.it/digit/
Chailyan, A., Tramontano, A., Marcatili, P. A database of immunogloblins with integrated tools: DIGIT Nucl. Acids Res. (2011) doi: 10.1093/nar/gkr806
Phospho3d: a database of three-dimensional structures of phosphorylation sites
http://arianna.bio.uniroma1.it/phospho3d/
Zanzoni A., Carbajo D., Diella F., Gherardini P.F., Tramontano A., Helmer-Citterich M., Via A. Phospho3D 2.0: An enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res. (in press)
PICMI: A tool to map nucleotide and amino acid variations on genomes and on all gene isoforms:
http://www.biocomputing.it/picmi
Le Pera, L., Marcatili, P., Tramontano, A. Picmi: mapping point mutations on genomes, Bioinformatics 2010 Nov 15;26(22):2904-5
SLEP: An automatic method for identifying surface proteins in bacteria:
Giombini, E., Orsini, M., Carabino, D. and Tramontano, A. An automatic method for identifying surface proteins in bacteria: SLEP (2010) BMC Bioinformatics 2010, 11:39
PIGS: Prediction of Immunoglobulin Structures
Marcatili, P., Rosi, A. and Tramontano, A. PIGS: Automatic prediction of antibody structures (2008) Bioinformatics, 24(17):1953-1954.
Maistas: Prediction of structure of alternative splicing isoforms in eukaryotic genomes
http://www.bioinformatica.crs4.org/maistas/
PMDB: A database of manually built models
Castrignano', T., D'Onorio De Meo, P., Cozzetto, D., Talamo, I. and Tramontano, A. 2006. The PMDB Protein Model Database Nuclei Acids Research, 34, 306-309
MOVIN: PPI interaction maps analyis tool
Marcatili, P., Bussotti, G., Tramontano, A. The MoVin server (2008) BMC Bioinformatics, 9:S11
Meps and MapMep: Mapping epitopes on protein surfaces
Castrignano', T., D'Onorio De Meo, P., Carrabino, D., Orsini, M., Floris, M. and Tramontano, A. The MEPS server for identifying protein conformational epitopes, (2007) BMC Bioinformatics 10:1186/1471-2105-8-S1-s&
Carrabino, D., D'Onorio De Meo, P., Sanna, N., Castrignano', T. Orsini, M., Floris, M. and Tramontano, A. The mepsMAP server (2007) IEEE Transactions on nanobiosciences, 6(2),155-161
Please let us know if you encounter any problem in using them...
