SMART: identification and annotation of domains from signalling and extracellular protein sequences - PubMed (original) (raw)
SMART: identification and annotation of domains from signalling and extracellular protein sequences
C P Ponting et al. Nucleic Acids Res. 1999.
Abstract
SMART is a simple modular architecture research tool and database that provides domain identification and annotation on the WWW (http://coot.embl-heidelberg.de/SMART). The tool compares query sequences with its databases of domain sequences and multiple alignments whilst concurrently identifying compositionally biased regions such as signal peptide, transmembrane and coiled coil segments. Annotated and unannotated regions of the sequence can be used as queries in searches of sequence databases. The SMART alignment collection represents more than 250 signalling and extracellular domains. Each alignment is curated to assign appropriate domain boundaries and to ensure its quality. In addition, each domain is annotated extensively with respect to cellular localisation, species distribution, functional class, tertiary structure and functionally important residues.
Similar articles
- Recent improvements to the SMART domain-based sequence annotation resource.
Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P. Letunic I, et al. Nucleic Acids Res. 2002 Jan 1;30(1):242-4. doi: 10.1093/nar/30.1.242. Nucleic Acids Res. 2002. PMID: 11752305 Free PMC article. - SMART: a web-based tool for the study of genetically mobile domains.
Schultz J, Copley RR, Doerks T, Ponting CP, Bork P. Schultz J, et al. Nucleic Acids Res. 2000 Jan 1;28(1):231-4. doi: 10.1093/nar/28.1.231. Nucleic Acids Res. 2000. PMID: 10592234 Free PMC article. - Database of protein sequence alignments: PIR-ALN.
Srinivasarao GY, Yeh LS, Marzec CR, Orcutt BC, Barker WC, Pfeiffer F. Srinivasarao GY, et al. Nucleic Acids Res. 1999 Jan 1;27(1):284-5. doi: 10.1093/nar/27.1.284. Nucleic Acids Res. 1999. PMID: 9847202 Free PMC article. - Detecting atypical examples of known domain types by sequence similarity searching: the SBASE domain library approach.
Dhir S, Pacurar M, Franklin D, Gáspári Z, Kertész-Farkas A, Kocsor A, Eisenhaber F, Pongor S. Dhir S, et al. Curr Protein Pept Sci. 2010 Nov;11(7):538-49. doi: 10.2174/138920310794109148. Curr Protein Pept Sci. 2010. PMID: 20887262 Review. - Comparative methods for identifying functional domains in protein sequences.
Henikoff S. Henikoff S. Biotechnol Annu Rev. 1995;1:129-47. doi: 10.1016/s1387-2656(08)70050-4. Biotechnol Annu Rev. 1995. PMID: 9704087 Review.
Cited by
- Genetic evidence links the ASTRA protein chaperone component Tti2 to the SAGA transcription factor Tra1.
Genereaux J, Kvas S, Dobransky D, Karagiannis J, Gloor GB, Brandl CJ. Genereaux J, et al. Genetics. 2012 Jul;191(3):765-80. doi: 10.1534/genetics.112.140459. Epub 2012 Apr 13. Genetics. 2012. PMID: 22505622 Free PMC article. - Genome-Wide Characterization, Evolution, and Expression Analysis of the Leucine-Rich Repeat Receptor-Like Protein Kinase (LRR-RLK) Gene Family in Medicago truncatula.
Meng J, Yang J, Peng M, Liu X, He H. Meng J, et al. Life (Basel). 2020 Sep 4;10(9):176. doi: 10.3390/life10090176. Life (Basel). 2020. PMID: 32899802 Free PMC article. - MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC. Edgar RC. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. doi: 10.1093/nar/gkh340. Print 2004. Nucleic Acids Res. 2004. PMID: 15034147 Free PMC article. - LOC3D: annotate sub-cellular localization for protein structures.
Nair R, Rost B. Nair R, et al. Nucleic Acids Res. 2003 Jul 1;31(13):3337-40. doi: 10.1093/nar/gkg514. Nucleic Acids Res. 2003. PMID: 12824321 Free PMC article. - Vaccination with recombinant oncosphere antigens reduces the susceptibility of sheep to infection with Taenia multiceps.
Gauci C, Vural G, Oncel T, Varcasia A, Damian V, Kyngdon CT, Craig PS, Anderson GA, Lightowlers MW. Gauci C, et al. Int J Parasitol. 2008 Jul;38(8-9):1041-50. doi: 10.1016/j.ijpara.2007.11.006. Epub 2007 Nov 24. Int J Parasitol. 2008. PMID: 18160069 Free PMC article. Clinical Trial.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources