ReviewThe Journal of biological chemistry2012
Inference of functional properties from large-scale analysis of enzyme superfamilies.
Review in The Journal of biological chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed.
- Genome-Wide Analysis of the Common Fig (Ficus carica L.) R2R3-MYB Genes Reveals Their Structure, Evolution, and Roles in Fruit Color Variation.Biochemical genetics · 2025Article
- Identifying protein function and functional links based on large-scale co-occurrence patterns.PloS one · 2022Article
- Discovery of novel glycoside hydrolases from C-glycoside-degrading bacteria using sequence similarity network analysis.Journal of microbiology (Seoul, Korea) · 2021Article
- PhotoModPlus: A web server for photosynthetic protein prediction from genome neighborhood features.PloS one · 2021Article
- Functional Annotation of ABHD14B, an Orphan Serine Hydrolase Enzyme.Biochemistry · 2020Article
- The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways.Biochemistry · 2019Article
- Effusion: prediction of protein function from sequence similarity networks.Bioinformatics (Oxford, England) · 2019Article
- Evolutionary Relationships Between Low Potential Ferredoxin and Flavodoxin Electron Carriers.Frontiers in energy research · 2019Article
- The GMC superfamily of oxidoreductases revisited: analysis and evolution of fungal GMC oxidoreductases.Biotechnology for biofuels · 2019Article
- A global view of structure-function relationships in the tautomerase superfamily.The Journal of biological chemistry · 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
- Cytochromes P450 for natural product biosynthesis in Streptomyces: sequence, structure, and function.Natural product reports · 2017Review
- A prominent glycyl radical enzyme in human gut microbiomes metabolizesScience (New York, N.Y.) · 2017Article
- Comparative Protein Structure Modeling Using MODELLER.Current protocols in bioinformatics · 2016Article
- Genome neighborhood network reveals insights into enediyne biosynthesis and facilitates prediction and prioritization for discovery.Journal of industrial microbiology & biotechnology · 2016Article
- Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.Biochimica et biophysica acta · 2015Review
- Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.Chemical Society reviews · 2015Review
- A transient receptor potential ion channel in Chlamydomonas shares key features with sensory transduction-associated TRP channels in mammals.The Plant cell · 2015Article
- The evolution of enzyme function in the isomerases.Current opinion in structural biology · 2014Review
- The Structure-Function Linkage Database.Nucleic acids research · 2014Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
As increasingly large amounts of data from genome and other sequencing projects become available, new approaches are needed to determine the functions of the proteins these genes encode. We show how large-scale computational analysis can help to address this challenge by linking functional information to sequence and structural similarities using protein similarity networks. Network analyses using three functionally diverse enzyme superfamilies illustrate the use of these approaches for facile updating and comparison of available structures for a large superfamily, for creation of functional hypotheses for metagenomic sequences, and to summarize the limits of our functional knowledge about even well studied superfamilies.
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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.