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Searching the protein interaction space through the MINT database.
Chatr-Aryamontri A, Zanzoni A, Ceol A, Cesareni G. Chatr-Aryamontri A, et al. Among authors: zanzoni a. Methods Mol Biol. 2008;484:305-17. doi: 10.1007/978-1-59745-398-1_20. Methods Mol Biol. 2008. PMID: 18592188
Protein-protein interaction databases are thus becoming a major resource for investigating biological networks and pathways. ...The MINT database aims at storing, in a structured format, information about protein-protein interactions (PPIs) by extracting experimenta …
Protein-protein interaction databases are thus becoming a major resource for investigating biological networks and pathways. ...The M …
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites.
Zanzoni A, Ausiello G, Via A, Gherardini PF, Helmer-Citterich M. Zanzoni A, et al. Nucleic Acids Res. 2007 Jan;35(Database issue):D229-31. doi: 10.1093/nar/gkl922. Epub 2006 Nov 16. Nucleic Acids Res. 2007. PMID: 17142231 Free PMC article.
Here we present Phospho3D, http://cbm.bio.uniroma2.it/phospho3d, a database of 3D structures of phosphorylation sites, which stores information retrieved from the phospho.ELM database and is enriched with structural information and annotations at the residue level. The dat …
Here we present Phospho3D, http://cbm.bio.uniroma2.it/phospho3d, a database of 3D structures of phosphorylation sites, which stores i …
pdbFun: mass selection and fast comparison of annotated PDB residues.
Ausiello G, Zanzoni A, Peluso D, Via A, Helmer-Citterich M. Ausiello G, et al. Among authors: zanzoni a. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W133-7. doi: 10.1093/nar/gki499. Nucleic Acids Res. 2005. PMID: 15980442 Free PMC article.
For example a search could involve, as a query, all solvent-exposed, hydrophylic residues that are not in alpha-helices and are involved in nucleotide binding. Possible examples of targets are represented by another selection, a single structure or a d …
For example a search could involve, as a query, all solvent-exposed, hydrophylic residues that are not in alpha-helices and ar …
Seq2Struct: a resource for establishing sequence-structure links.
Via A, Zanzoni A, Helmer-Citterich M. Via A, et al. Among authors: zanzoni a. Bioinformatics. 2005 Feb 15;21(4):551-3. doi: 10.1093/bioinformatics/bti049. Epub 2004 Sep 28. Bioinformatics. 2005. PMID: 15454411
In this study, we describe Seq2Struct, a web resource for the identification of sequence-structure links. The resource consists of an exhaustive collection of annotated links between Swiss-Prot + TrEMBL and PDB + SCOP database entries. Links are based on pre-established hi …
In this study, we describe Seq2Struct, a web resource for the identification of sequence-structure links. The resource consists of an …
MINT: a Molecular INTeraction database.
Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, Cesareni G. Zanzoni A, et al. FEBS Lett. 2002 Feb 20;513(1):135-40. doi: 10.1016/s0014-5793(01)03293-8. FEBS Lett. 2002. PMID: 11911893 Review.
Here we present MINT, a database (http://cbm.bio.uniroma2.it/mint/index.html) designed to store data on functional interactions between proteins. ...MINT consists of entries extracted from the scientific literature by expert curators assisted by 'MINT Assistant', a
Here we present MINT, a database (http://cbm.bio.uniroma2.it/mint/index.html) designed to store data on functional interactions betwe …
SURFACE: a database of protein surface regions for functional annotation.
Ferrè F, Ausiello G, Zanzoni A, Helmer-Citterich M. Ferrè F, et al. Among authors: zanzoni a. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D240-4. doi: 10.1093/nar/gkh054. Nucleic Acids Res. 2004. PMID: 14681403 Free PMC article.
SURFACE contains the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. ...A n …
SURFACE contains the results of a large-scale protein annotation and local structural comparison project. A non-redundant set …
Development of computational tools for the inference of protein interaction specificity rules and functional annotation using structural information.
Ferrè F, Via A, Ausiello G, Brannetti B, Zanzoni A, Helmer-Citterich M. Ferrè F, et al. Among authors: zanzoni a. Comp Funct Genomics. 2003;4(4):416-9. doi: 10.1002/cfg.304. Comp Funct Genomics. 2003. PMID: 18629081 Free PMC article.
We analyse the structures of proteins encoding a function specified in a PROSITE pattern, which exhibits relatively low selectivity and specificity, and build extended patterns. ...We also analyse protein surface regions and, through the annotation of the solvent-ex …
We analyse the structures of proteins encoding a function specified in a PROSITE pattern, which exhibits relatively low select …
Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites.
Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A. Zanzoni A, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D268-71. doi: 10.1093/nar/gkq936. Epub 2010 Oct 21. Nucleic Acids Res. 2011. PMID: 20965970 Free PMC article.
The database also provides the results of a large-scale structural comparison of the 3D zones versus a representative dataset of structures, thus associating to each P-site a number of structurally similar sites. ...Moreover, it features P3Dscan, a new …
The database also provides the results of a large-scale structural comparison of the 3D zones versus a representative dataset …
iSPOT: a web tool for the analysis and recognition of protein domain specificity.
Brannetti B, Zanzoni A, Montecchi-Palazzi L, Cesareni G, Helmer-Citterich M. Brannetti B, et al. Among authors: zanzoni a. Comp Funct Genomics. 2001;2(5):314-8. doi: 10.1002/cfg.104. Comp Funct Genomics. 2001. PMID: 18629248 Free PMC article.
Methods that aim at predicting interaction partners are very likely to play an important role in the interpretation of genomic information. iSPOT (iSpecificity Prediction Of Target) is a web tool (accessible at http://cbm.bio.uniroma2.it/iSPOT) developed for the prediction …
Methods that aim at predicting interaction partners are very likely to play an important role in the interpretation of genomic information. …
Systematic identification of molecular links between core and candidate genes in breast cancer.
Arroyo R, Suñé G, Zanzoni A, Duran-Frigola M, Alcalde V, Stracker TH, Soler-López M, Aloy P. Arroyo R, et al. Among authors: zanzoni a. J Mol Biol. 2015 Mar 27;427(6 Pt B):1436-1450. doi: 10.1016/j.jmb.2015.01.014. Epub 2015 Jan 29. J Mol Biol. 2015. PMID: 25640309
Our aim is to generate a protein interaction network of BC-associated gene products and suggest potential molecular mechanisms to unveil their role in the disease. ...Overall, our BC-related network may serve as a framework to integrate clinical and molecular data a …
Our aim is to generate a protein interaction network of BC-associated gene products and suggest potential molecular mechanisms to unv …
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