ArticleBioinformatics (Oxford, England)2013
Pclust: protein network visualization highlighting experimental data.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed, 7 citations in OpenAlex.
- Effusion: prediction of protein function from sequence similarity networks.Bioinformatics (Oxford, England) · 2019Article
- Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.Biochemistry · 2017Review
- Biocuration in the structure-function linkage database: the anatomy of a superfamily.Database : the journal of biological databases and curation · 2017Article
- Quo vadis computational analysis of PPI data or why the future isn't here yet.Frontiers in genetics · 2015Article
- SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
summaryOne approach to infer functions of new proteins from their homologs utilizes visualization of an all-against-all pairwise similarity network (A2ApsN) that exploits the speed of BLAST and avoids the complexity of multiple sequence alignment. However, identifying functions of the protein clusters in A2ApsN is never trivial, due to a lack of linking characterized proteins to their relevant information in current software packages. Given the database errors introduced by automatic annotation transfer, functional deduction should be made from proteins with experimental studies, i.e. 'reference proteins'. Here, we present a web server, termed Pclust, which provides a user-friendly interface to visualize the A2ApsN, placing emphasis on such 'reference proteins' and providing access to their full information in source databases, e.g. articles in PubMed. The identification of 'reference proteins' and the ease of cross-database linkage will facilitate understanding the functions of protein clusters in the network, thus promoting interpretation of proteins of interest. AVAILABILITY: The Pclust server is freely available at http://prodata.swmed.edu/pclust
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.