ReviewCurrent opinion in structural biology2009
Is protein classification necessary? Toward alternative approaches to function annotation.
Review in Current opinion in structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed.
- BioS2Net: Holistic Structural and Sequential Analysis of Biomolecules Using a Deep Neural Network.International journal of molecular sciences · 2022Article
- PvaxDB: a comprehensive structural repository of Plasmodium vivax proteome.Database : the journal of biological databases and curation · 2018Article
- Structural Bridges through Fold Space.PLoS computational biology · 2015Article
- Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.Protein science : a publication of the Protein Society · 2015Article
- Template-based prediction of protein function.Current opinion in structural biology · 2015Review
- Global view of the protein universe.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Structural bioinformatics of the interactome.Annual review of biophysics · 2014Review
- Article
- Toward a "structural BLAST": using structural relationships to infer function.Protein science : a publication of the Protein Society · 2013Review
- The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes.PLoS computational biology · 2012Article
- Protective gene expression changes elicited by an inherited defect in photoreceptor structure.PloS one · 2012Article
- Composite structural motifs of binding sites for delineating biological functions of proteins.PloS one · 2012Article
- Maps of protein structure space reveal a fundamental relationship between protein structure and function.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat.The Journal of cell biology · 2011Review
- Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold.Computational biology and chemistry · 2011Article
- Remote thioredoxin recognition using evolutionary conservation and structural dynamics.Structure (London, England : 1993) · 2011Article
- Article
- Structural space of protein-protein interfaces is degenerate, close to complete, and highly connected.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Issues in bioinformatics benchmarking: the case study of multiple sequence alignment.Nucleic acids research · 2010Review
- Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems.Theoretical biology & medical modelling · 2010Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
The current nonredundant protein sequence database contains over seven million entries and the number of individual functional domains is significantly larger than this value. The vast quantity of data associated with these proteins poses enormous challenges to any attempt at function annotation. Classification of proteins into sequence and structural groups has been widely used as an approach to simplifying the problem. In this article we question such strategies. We describe how the multifunctionality and structural diversity of even closely related proteins confounds efforts to assign function on the basis of overall sequence or structural similarity. Rather, we suggest that strategies that avoid classification may offer a more robust approach to protein function annotation.
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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.