ArticleNucleic acids research2008
SIMAP--structuring the network of protein similarities.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Signature protein of the PVC superphylum.Applied and environmental microbiology · 2014Article
- SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.Nucleic acids research · 2014Article
- The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.Nucleic acids research · 2011Article
- B2G-FAR, a species-centered GO annotation repository.Bioinformatics (Oxford, England) · 2011Article
- MIPS: curated databases and comprehensive secondary data resources in 2010.Nucleic acids research · 2011Article
- FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum.Nucleic acids research · 2011Article
- ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes.Bioinformatics (Oxford, England) · 2010Article
- The genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common mechanisms for host cell interaction among amoeba-associated bacteria.Journal of bacteriology · 2010Article
- Gene3D: merging structure and function for a Thousand genomes.Nucleic acids research · 2010Article
- Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae.BMC genomics · 2009Article
- Protein comparison at the domain architecture level.BMC bioinformatics · 2009Article
- An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D.BMC bioinformatics · 2009Article
- Sequence-based prediction of type III secreted proteins.PLoS pathogens · 2009Article
- PEDANT covers all complete RefSeq genomes.Nucleic acids research · 2009Article
- DAhunter: a web-based server that identifies homologous proteins by comparing domain architecture.Nucleic acids research · 2008Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein sequences are the most important source of evolutionary and functional information for new proteins. In order to facilitate the computationally intensive tasks of sequence analysis, the Similarity Matrix of Proteins (SIMAP) database aims to provide a comprehensive and up-to-date dataset of the pre-calculated sequence similarity matrix and sequence-based features like InterPro domains for all proteins contained in the major public sequence databases. As of September 2007, SIMAP covers approximately 17 million proteins and more than 6 million non-redundant sequences and provides a complete annotation based on InterPro 16. Novel features of SIMAP include a new, portlet-based web portal providing multiple, structured views on retrieved proteins and integration of protein clusters and a unique search method for similar domain architectures. Access to SIMAP is freely provided for academic use through the web portal for individuals at http://mips.gsf.de/simap/and through Web Services for programmatic access at http://mips.gsf.de/webservices/services/SimapService2.0?wsdl.
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