ArticleNucleic acids research2003
ProtoNet: hierarchical classification of the protein space.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- In silico functional and structural characterization revealed virulent proteins ofMolecular biology research communications · 2022Article
- Integrated bioinformatics based subtractive genomics approach to decipher the therapeutic function of hypothetical proteins from Salmonella typhi XDR H-58 strain.Biotechnology letters · 2022Article
- Article
- Structural and functional annotation of hypothetical proteins of human adenovirus: prioritizing the novel drug targets.BMC research notes · 2017Article
- Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution.Trends in microbiology · 2016Review
- Chitinase from Thermomyces lanuginosus SSBP and its biotechnological applications.Extremophiles : life under extreme conditions · 2015Review
- Trends in genome dynamics among major orders of insects revealed through variations in protein families.BMC genomics · 2015Article
- ProtoBug: functional families from the complete proteomes of insects.Database : the journal of biological databases and curation · 2015Article
- Entropy-driven partitioning of the hierarchical protein space.Bioinformatics (Oxford, England) · 2014Article
- A pluralistic account of homology: adapting the models to the data.Molecular biology and evolution · 2014Review
- Whole-proteome analysis of twelve species of alphaproteobacteria links four pathogens.Pathogens (Basel, Switzerland) · 2013Article
- Functional inference by ProtoNet family tree: the uncharacterized proteome of Daphnia pulex.BMC bioinformatics · 2013Article
- Ultrafast clustering algorithms for metagenomic sequence analysis.Briefings in bioinformatics · 2012Article
- Article
- ProtoNet 6.0: organizing 10 million protein sequences in a compact hierarchical family tree.Nucleic acids research · 2012Article
- clusterMaker: a multi-algorithm clustering plugin for Cytoscape.BMC bioinformatics · 2011Article
- Family classification without domain chaining.Bioinformatics (Oxford, England) · 2009Article
- Michigan molecular interactions r2: from interacting proteins to pathways.Nucleic acids research · 2009Article
- Article
- Insight into the haem d1 biosynthesis pathway in heliobacteria through bioinformatics analysis.Microbiology (Reading, England) · 2007Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outcome of this clustering process is a classification of the input proteins into a hierarchy of clusters of varying degrees of granularity. ProtoNet (version 1.3) is accessible in the form of an interactive web site at http://www.protonet.cs.huji.ac.il. ProtoNet provides navigation tools for monitoring the clustering process with a vertical and horizontal view. Each cluster at any level of the hierarchy is assigned with a statistical index, indicating the level of purity based on biological keywords such as those provided by SWISS-PROT and InterPro. ProtoNet can be used for function prediction, for defining superfamilies and subfamilies and for large-scale protein annotation purposes.
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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.