ArticleNucleic acids research2005
ProtoNet 4.0: a hierarchical classification of one million protein sequences.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Clustering analysis of proteins from microbial genomes at multiple levels of resolution.BMC bioinformatics · 2016Article
- Trends in genome dynamics among major orders of insects revealed through variations in protein families.BMC genomics · 2015Article
- Entropy-driven partitioning of the hierarchical protein space.Bioinformatics (Oxford, England) · 2014Article
- Functional clustering of immunoglobulin superfamily proteins with protein-protein interaction information calibrated hidden Markov model sequence profiles.Journal of molecular biology · 2014Article
- Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex.BMC bioinformatics · 2013Article
- SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation.Database : the journal of biological databases and curation · 2013Article
- How to inherit statistically validated annotation within BAR+ protein clusters.BMC bioinformatics · 2013Article
- DAMPD: a manually curated antimicrobial peptide database.Nucleic acids research · 2012Article
- ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree.Nucleic acids research · 2012Article
- Ortholog identification in the presence of domain architecture rearrangement.Briefings in bioinformatics · 2011Review
- BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences.Nucleic acids research · 2011Article
- Genome-wide comparative gene family classification.PloS one · 2010Article
- A predictor for toxin-like proteins exposes cell modulator candidates within viral genomes.Bioinformatics (Oxford, England) · 2010Article
- PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations.Nucleic acids research · 2010Article
- GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains.Nucleic acids research · 2010Article
- ESG: extended similarity group method for automated protein function prediction.Bioinformatics (Oxford, England) · 2009Article
- ClanTox: a classifier of short animal toxins.Nucleic acids research · 2009Article
- Partitioning clustering algorithms for protein sequence data sets.BioData mining · 2009Article
- Genome and proteome annotation: organization, interpretation and integration.Journal of the Royal Society, Interface · 2009Review
- Protein function annotation by homology-based inference.Genome biology · 2009Review
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9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
ProtoNet is an automatic hierarchical classification of the protein sequence space. In 2004, the ProtoNet (version 4.0) presents the analysis of over one million proteins merged from SwissProt and TrEMBL databases. In addition to rich visualization and analysis tools to navigate the clustering hierarchy, we incorporated several improvements that allow a simplified view of the scaffold of the proteins. An unsupervised, biologically valid method that was developed resulted in a condensation of the ProtoNet hierarchy to only 12% of the clusters. A large portion of these clusters was automatically assigned high confidence biological names according to their correspondence with functional annotations. ProtoNet is available at: http://www.protonet.cs.huji.ac.il.
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