ArticleBioinformatics (Oxford, England)2012
Pythoscape: a framework for generation of large protein similarity networks.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
37 citing papers in PubMed.
- Review
- Human SIRT1 Multispecificity Is Modulated by Active-Site Vicinity Substitutions during Natural Evolution.Molecular biology and evolution · 2021Article
- Structural Basis for the Asymmetry of a 4-Oxalocrotonate Tautomerase Trimer.Biochemistry · 2020Article
- A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function.Database : the journal of biological databases and curation · 2020Article
- Structural and Biochemical Insights Into Two BAHD Acyltransferases (Frontiers in plant science · 2020Article
- The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways.Biochemistry · 2019Article
- Oxidative opening of the aromatic ring: Tracing the natural history of a large superfamily of dioxygenase domains and their relatives.The Journal of biological chemistry · 2019Article
- Structural, Kinetic, and Mechanistic Analysis of an Asymmetric 4-Oxalocrotonate Tautomerase Trimer.Biochemistry · 2019Article
- Effusion: prediction of protein function from sequence similarity networks.Bioinformatics (Oxford, England) · 2019Article
- 'Democratized' genomic enzymology web tools for functional assignment.Current opinion in chemical biology · 2018Review
- A global view of structure-function relationships in the tautomerase superfamily.The Journal of biological chemistry · 2018Article
- Article
- Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a "Plug and Play" Domain.Methods in enzymology · 2018Article
- Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Structural and Chemical Biology of Terpenoid Cyclases.Chemical reviews · 2017Review
- 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
- Evaluating Functional Annotations of Enzymes Using the Gene Ontology.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Molecular Diversity of Terpene Synthases in the Liverwort Marchantia polymorpha.The Plant cell · 2016Article
- Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.Biochimica et biophysica acta · 2015Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Pythoscape is a framework implemented in Python for processing large protein similarity networks for visualization in other software packages. Protein similarity networks are graphical representations of sequence, structural and other similarities among proteins for which pairwise all-by-all similarity connections have been calculated. Mapping of biological and other information to network nodes or edges enables hypothesis creation about sequence-structure-function relationships across sets of related proteins. Pythoscape provides several options to calculate pairwise similarities for input sequences or structures, applies filters to network edges and defines sets of similar nodes and their associated data as single nodes (termed representative nodes) for compression of network information and output data or formatted files for visualization.
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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.