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Items: 1 to 20 of 169

1.

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.

2.

The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis.

Bartoli L, Montanucci L, Fronza R, Martelli PL, Fariselli P, Carota L, Donvito G, Maggi GP, Casadio R.

J Proteome Res. 2009 Sep;8(9):4362-71. doi: 10.1021/pr900204r.

PMID:
19552451
3.

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

Profiti G, Martelli PL, Casadio R.

Nucleic Acids Res. 2017 Apr 27. doi: 10.1093/nar/gkx330. [Epub ahead of print]

PMID:
28453653
4.

How to inherit statistically validated annotation within BAR+ protein clusters.

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

BMC Bioinformatics. 2013;14 Suppl 3:S4. doi: 10.1186/1471-2105-14-S3-S4. Epub 2013 Feb 28.

5.

The human "magnesome": detecting magnesium binding sites on human proteins.

Piovesan D, Profiti G, Martelli PL, Casadio R.

BMC Bioinformatics. 2012;13 Suppl 14:S10. doi: 10.1186/1471-2105-13-S14-S10. Epub 2012 Sep 7.

6.

The HHpred interactive server for protein homology detection and structure prediction.

Söding J, Biegert A, Lupas AN.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W244-8.

8.

SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation.

Piovesan D, Profiti G, Martelli PL, Fariselli P, Fontanesi L, Casadio R.

Database (Oxford). 2013 Sep 23;2013:bat065. doi: 10.1093/database/bat065. Print 2013.

9.
10.

CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences.

Chen X, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP.

BMC Bioinformatics. 2007 Apr 19;8:129.

11.
12.

webPRC: the Profile Comparer for alignment-based searching of public domain databases.

Brandt BW, Heringa J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W48-52. doi: 10.1093/nar/gkp279. Epub 2009 May 6.

13.

Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.

Terrapon N, Gascuel O, Maréchal E, Bréhélin L.

BMC Bioinformatics. 2012 May 1;13:67. doi: 10.1186/1471-2105-13-67.

14.

Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.

Ponomarenko JV, Bourne PE, Shindyalov IN.

Proteins. 2005 Mar 1;58(4):855-65.

PMID:
15645518
15.

PASS2: an automated database of protein alignments organised as structural superfamilies.

Bhaduri A, Pugalenthi G, Sowdhamini R.

BMC Bioinformatics. 2004 Apr 2;5:35.

16.

Uniclust databases of clustered and deeply annotated protein sequences and alignments.

Mirdita M, von den Driesch L, Galiez C, Martin MJ, Söding J, Steinegger M.

Nucleic Acids Res. 2017 Jan 4;45(D1):D170-D176. doi: 10.1093/nar/gkw1081. Epub 2016 Nov 28.

PMID:
27899574
17.

Gene3D: comprehensive structural and functional annotation of genomes.

Yeats C, Lees J, Reid A, Kellam P, Martin N, Liu X, Orengo C.

Nucleic Acids Res. 2008 Jan;36(Database issue):D414-8. Epub 2007 Nov 21.

18.

Bioverse: Functional, structural and contextual annotation of proteins and proteomes.

McDermott J, Samudrala R.

Nucleic Acids Res. 2003 Jul 1;31(13):3736-7.

19.

UFO: a web server for ultra-fast functional profiling of whole genome protein sequences.

Meinicke P.

BMC Genomics. 2009 Sep 2;10:409. doi: 10.1186/1471-2164-10-409.

20.

AlignHUSH: alignment of HMMs using structure and hydrophobicity information.

Krishnadev O, Srinivasan N.

BMC Bioinformatics. 2011 Jul 5;12:275. doi: 10.1186/1471-2105-12-275.

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