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Tools

 

We have developed a number of tools and scripts that you might find useful.

They are kept alive and mantained  for at least two years after publication of the related article. After that time, we will keep alive and mantain the tools that are still used, as judged from the references to the related paper. 


Pepcomposer

Website: http://biocomputing.it/pepcomposer/


LoopIng: a template-based tool for predicting the structure of protein loops

Website: http://biocomputing.it/looping/

Messih M.A., Lepore R., Tramontano A. (2015) LoopIng: a template-based tool for predicting the structure of protein loops. Bioinformatics. Aug 6. pii: btv438 (Epub ahead of print)


Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chain of antibodies

Website: http://www.biocomputing.it/H3Loopred/

Messih M.A., Lepore R., Marcatili P., Tramontano A. (2014) Improving the accuracy of the third hypervariable loop of the heavy chain of antibodies. Bioinformatics. Oct;30(19):2733-40. doi: 10.1093/bioinformatics/btu194


3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments

Website: http://www.biocomputing.it/3uss_server/

Le Pera L., Mazzapioda M., Tramontano A. (2015) 3USS: a web server for detecting alternative 3’UTRs from RNA-seq experiments. Bioinformatics. First published online January 22, 2015.


Tabhu: Tool for AntiBody Humanization

Website http://www.biocomputing.it/tabhu

Olimpieri P.P., Marcatili P. and Tramontano A. (2015) Tabhu: tools for antibody humanization. In press. doi:10.1093/bioinformatics/btt369


TiPs: a database of therapeutic targets in pathogens and associated tools

Websitehttp://www.biocomputing.it/tips

Lepore R., Tramontano A., Via A. (2013) TiPs: a database of therapeutic targets in pathogens and associated tools. Bioinformatics 29(14):1821-2. doi: 10.1093/bioinformatics/btt289


proABC for the predicition of site-specific interactions in antibody-antigen complexes

Websitehttp://www.biocomputing.it/proABC

Olimpieri P.P., Chailyan A., Tramontano A. and Marcatili P. (2013) Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server. Bioinformatics 29(18):2285-91. doi:10.1093/bioinformatics/btt369


FIDEA, a web server designed to facilitate the functional interpretation of differential expression analysis

Websitehttp://www.biocomputing.it/fidea

D'Andrea D., Grassi L., Mazzapioda M. and Tramontano A. (2013) FIDEA: a server for the functional interpretation of differential expression analysis. Nucleic Acids Res. 41 (W1): W84-W88. doi:10.1093/nar/gkt516


MODalign: A tool to display, evaluate and edit alignments for comparative modeling

Websitehttp://modorama.org

Barbato A., Benkert P., Schwede T., Tramontano A. and Kosinski J. (2012)  Improving your target-template alignment with MODalign. Bioinformatics 28 (7):1038-1039. doi:10.1093/bioinformatics/bts070


MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships

Website http://modorama.org

Kosinski J., Barbato A., Tramontano A. (2013) MODexplorer: an integrated tool for exploring protein sequence, structure and function relationships Bioinformatics 29(7): 953-954. doi:10.1093/bioinformatics/btt062


DIGIT: a database of immunoglobulin variable domain sequences

Website http://www.biocomputing.it/digit/

Chailyan A., Tramontano A., Marcatili P. (2012) A database of immunoglobulins with integrated tools: DIGIT. Nucleic Acids Research 40:D1230-D1234. doi:10.1093/nar/gkr806


PIGS: Prediction of Immunoglobulin Structures

Website www.biocomputing.it/pigs

1. Marcatili P., Rosi A. and Tramontano A. (2008) PIGS: Automatic prediction of antibody structures Bioinformatics, 24(17):1953-1954. doi:10.1093/bioinformatics/btn341

2. Marcatili, P., Olimpieri, P. P., Chailyan, A., & Tramontano, A. (2014). Antibody modeling using the Prediction of ImmunoGlobulin Structure (PIGS) web server. Nature protocols9(12), 2771-2783. doi:10.1038/nprot.2014.189


Phospho3d: a database of three-dimensional structures of phosphorylation sites

Websitehttp://www.phospho3d.org/

Zanzoni A., Carbajo D., Diella F., Gherardini P.F., Tramontano A., Helmer-Citterich M., Via A. (2011) Phospho3D 2.0: An enhanced database of three-dimensional structures of phosphorylation sites. Nucleic Acids Res. 39: D268-71. doi:10.1093/nar/gkq936


PICMI: A tool to map nucleotide and amino acid variations on genomes and on all gene isoforms

Websitehttp://www.biocomputing.it/picmi

Le Pera L., Marcatili P., Tramontano A. (2010) Picmi: mapping point mutations on genomes. Bioinformatics 26(22): 2904-5. doi:10.1093/bioinformatics/btq547


Maistas: Prediction of structure of alternative splicing isoforms in eukaryotic genomes

Websitehttp://maistas.bioinformatica.crs4.it/

Floris M., Raimondo D., Leoni G., Orsini M., Marcatili P. and Tramontano A. (2011) MAISTAS: a tool for automatic structural evaluation of alternative splicing products. Bioinformatics 79(5): 1513–1524. doi:10.1093/bioinformatics/btr198


PMDB: A database of manually built models

Websitehttps://bioinformatics.cineca.it/PMDB/

Castrignanò T., De Meo P.D., Cozzetto D., Talamo I.G., Tramontano A. (2006) Nucleic Acids Res. 34(Database issue):D306-9. doi:10.1093/nar/gkj105


SLEP: An automatic method for identifying surface proteins in bacteria

Website: The web server availability period has expired

Giombini E., Orsini M., Carabino D. and Tramontano A. (2010) An automatic method for identifying surface proteins in bacteria: SLEP BMC Bioinformatics 11:39. doi:10.1186/1471-2105-11-39


MOVIN: PPI interaction maps analyis tool

Website: The web server availability period has expired

Marcatili P., Bussotti G., Tramontano A. (2008) The MoVin server BMC Bioinformatics 9:S11. doi:10.1186/1471-2105-9-S2-S11


ESTRELLA: designed to characterize mutually exclusive interactors

Website: The web server availability period has expired

Sánchez Claros, C. and  Tramontano, A. Detecting mutually exclusive interactions in protein-protein interaction maps (2012) PLoS One 7(6):e38765. doi:10.1371/journal.pone.0038765


Meps and MapMep: Mapping epitopes on protein surfaces

Website:The web server availability period has expired

Meps:

Castrignanò, 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&

mepsMAP:

Carrabino, D., D'Onorio De Meo, P., Sanna, N., Castrignanò, T. Orsini, M., Floris, M. and Tramontano, A. The mepsMAP server (2007) IEEE Transactions on nanobiosciences, 6(2),155-161.


MoDiPath: a comprehensive and freely accessible resource collecting linear motifs involved in signaling and metabolic pathways in several organisms

WebsiteThe web server availability period has expired

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. doi: 10.1371/journal.pone.0022270


ModelDB: A resource for benchmarking the usefulness of protein structure models

Website: The web server availability period has expired

Carbajo, D. and Tramontano, A. A resource forbenchmarking the usefulness of protein structure models. BMCBioinformatics (2012) 13:188. doi: 10.1186/1471-2105-13-188.


Scripts 

Scripts related to Guerreri et al.  

NED_description_forWEB

Ned_0.13

example_peaks

refSeq_hg19

Scripts related to Gandolfi et al.

http://arianna.med.uniroma1.it/epigenome_pipeline/Processing_Pipeline_Epigenome.zip

Last Updated ( Sunday, 25 December 2016 09:47 )