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Items: 1 to 20 of 119

1.

PANADA: protein association network annotation, determination and analysis.

Martin AJ, Walsh I, Domenico TD, Mičetić I, Tosatto SC.

PLoS One. 2013 Nov 12;8(11):e78383. doi: 10.1371/journal.pone.0078383. eCollection 2013.

2.

INGA: protein function prediction combining interaction networks, domain assignments and sequence similarity.

Piovesan D, Giollo M, Leonardi E, Ferrari C, Tosatto SC.

Nucleic Acids Res. 2015 Jul 1;43(W1):W134-40. doi: 10.1093/nar/gkv523. Epub 2015 May 27.

3.

NatalieQ: a web server for protein-protein interaction network querying.

El-Kebir M, Brandt BW, Heringa J, Klau GW.

BMC Syst Biol. 2014 Apr 1;8:40. doi: 10.1186/1752-0509-8-40.

4.

BIOVERSE: enhancements to the framework for structural, functional and contextual modeling of proteins and proteomes.

McDermott J, Guerquin M, Frazier Z, Chang AN, Samudrala R.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W324-5.

5.

RING: networking interacting residues, evolutionary information and energetics in protein structures.

Martin AJ, Vidotto M, Boscariol F, Di Domenico T, Walsh I, Tosatto SC.

Bioinformatics. 2011 Jul 15;27(14):2003-5. doi: 10.1093/bioinformatics/btr191. Epub 2011 Apr 14.

6.

CSpritz: accurate prediction of protein disorder segments with annotation for homology, secondary structure and linear motifs.

Walsh I, Martin AJ, Di Domenico T, Vullo A, Pollastri G, Tosatto SC.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W190-6. doi: 10.1093/nar/gkr411. Epub 2011 Jun 6.

7.

The integration and annotation of the human interactome in the UniHI Database.

Chaurasia G, Futschik M.

Methods Mol Biol. 2012;812:175-88. doi: 10.1007/978-1-61779-455-1_10.

PMID:
22218860
8.

L-GRAAL: Lagrangian graphlet-based network aligner.

Malod-Dognin N, Pržulj N.

Bioinformatics. 2015 Jul 1;31(13):2182-9. doi: 10.1093/bioinformatics/btv130. Epub 2015 Feb 28.

9.

Alignment-Annotator web server: rendering and annotating sequence alignments.

Gille C, Fähling M, Weyand B, Wieland T, Gille A.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W3-6. doi: 10.1093/nar/gku400. Epub 2014 May 9.

10.
11.

BisoGenet: a new tool for gene network building, visualization and analysis.

Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, Bringas R.

BMC Bioinformatics. 2010 Feb 17;11:91. doi: 10.1186/1471-2105-11-91.

12.

NetworkAnalyst--integrative approaches for protein-protein interaction network analysis and visual exploration.

Xia J, Benner MJ, Hancock RE.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W167-74. doi: 10.1093/nar/gku443. Epub 2014 May 26.

13.

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.

Piovesan D, Martelli PL, Fariselli P, Zauli A, Rossi I, Casadio R.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W197-202. doi: 10.1093/nar/gkr292. Epub 2011 May 26.

14.

cddApp: a Cytoscape app for accessing the NCBI conserved domain database.

Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE.

Bioinformatics. 2015 Jan 1;31(1):134-6. doi: 10.1093/bioinformatics/btu605. Epub 2014 Sep 10.

15.

The SSEA server for protein secondary structure alignment.

Fontana P, Bindewald E, Toppo S, Velasco R, Valle G, Tosatto SC.

Bioinformatics. 2005 Feb 1;21(3):393-5. Epub 2004 Sep 3.

16.

WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation.

Capriotti E, Calabrese R, Fariselli P, Martelli PL, Altman RB, Casadio R.

BMC Genomics. 2013;14 Suppl 3:S6. doi: 10.1186/1471-2164-14-S3-S6. Epub 2013 May 28.

17.

The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search.

Havgaard JH, Lyngsø RB, Gorodkin J.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W650-3.

18.

The IntAct molecular interaction database in 2012.

Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6. doi: 10.1093/nar/gkr1088. Epub 2011 Nov 24.

19.

miRClassify: an advanced web server for miRNA family classification and annotation.

Zou Q, Mao Y, Hu L, Wu Y, Ji Z.

Comput Biol Med. 2014 Feb;45:157-60. doi: 10.1016/j.compbiomed.2013.12.007. Epub 2013 Dec 21.

PMID:
24480175
20.

The MiSink Plugin: Cytoscape as a graphical interface to the Database of Interacting Proteins.

Salwinski L, Eisenberg D.

Bioinformatics. 2007 Aug 15;23(16):2193-5. Epub 2007 Jun 6.

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