Gherardini PF - Search Results

1

Artificial intelligence methods enhance the discovery of RNA interactions.

Pepe G, Appierdo R, Carrino C, Ballesio F, Helmer-Citterich M, Gherardini PF. Pepe G, et al. Among authors: gherardini pf. Front Mol Biosci. 2022 Oct 7;9:1000205. doi: 10.3389/fmolb.2022.1000205. eCollection 2022. Front Mol Biosci. 2022. PMID: 36275611 Free PMC article. Review.

2

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. Among authors: gherardini pf. 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.

3

False occurrences of functional motifs in protein sequences highlight evolutionary constraints.

Via A, Gherardini PF, Ferraro E, Ausiello G, Scalia Tomba G, Helmer-Citterich M. Via A, et al. Among authors: gherardini pf. BMC Bioinformatics. 2007 Mar 1;8:68. doi: 10.1186/1471-2105-8-68. BMC Bioinformatics. 2007. PMID: 17331242 Free PMC article.

4

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures.

Via A, Peluso D, Gherardini PF, de Rinaldis E, Colombo T, Ausiello G, Helmer-Citterich M. Via A, et al. Among authors: gherardini pf. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W416-9. doi: 10.1093/nar/gkm228. Epub 2007 May 8. Nucleic Acids Res. 2007. PMID: 17488847 Free PMC article.

5

Convergent evolution of enzyme active sites is not a rare phenomenon.

Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ. Gherardini PF, et al. J Mol Biol. 2007 Sep 21;372(3):817-45. doi: 10.1016/j.jmb.2007.06.017. Epub 2007 Jun 14. J Mol Biol. 2007. PMID: 17681532

6

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.

Ausiello G, Gherardini PF, Marcatili P, Tramontano A, Via A, Helmer-Citterich M. Ausiello G, et al. Among authors: gherardini pf. BMC Bioinformatics. 2008 Mar 26;9 Suppl 2(Suppl 2):S2. doi: 10.1186/1471-2105-9-S2-S2. BMC Bioinformatics. 2008. PMID: 18387204 Free PMC article.

7

Structure-based function prediction: approaches and applications.

Gherardini PF, Helmer-Citterich M. Gherardini PF, et al. Brief Funct Genomic Proteomic. 2008 Jul;7(4):291-302. doi: 10.1093/bfgp/eln030. Epub 2008 Jul 3. Brief Funct Genomic Proteomic. 2008. PMID: 18599513 Review.

8

Structural motifs recurring in different folds recognize the same ligand fragments.

Ausiello G, Gherardini PF, Gatti E, Incani O, Helmer-Citterich M. Ausiello G, et al. Among authors: gherardini pf. BMC Bioinformatics. 2009 Jun 15;10:182. doi: 10.1186/1471-2105-10-182. BMC Bioinformatics. 2009. PMID: 19527512 Free PMC article.

9

Modular architecture of nucleotide-binding pockets.

Gherardini PF, Ausiello G, Russell RB, Helmer-Citterich M. Gherardini PF, et al. Nucleic Acids Res. 2010 Jun;38(11):3809-16. doi: 10.1093/nar/gkq090. Epub 2010 Feb 25. Nucleic Acids Res. 2010. PMID: 20185567 Free PMC article.

10

Superpose3D: a local structural comparison program that allows for user-defined structure representations.

Gherardini PF, Ausiello G, Helmer-Citterich M. Gherardini PF, et al. PLoS One. 2010 Aug 5;5(8):e11988. doi: 10.1371/journal.pone.0011988. PLoS One. 2010. PMID: 20700534 Free PMC article.

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