ReviewCurrent opinion in structural biology2009
Nothing about protein structure classification makes sense except in the light of evolution.
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 22 papers.
What it found
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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.
The trial behind it
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
22 citing papers in PubMed.
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- Insights into virulence: structure classification of themSystems · 2023Article
- On Citing Dobzhansky about the Significance of Evolution to Biology.Integrative organismal biology (Oxford, England) · 2023Article
- Unraveling the structural landscape of intra-chain domain interfaces: Implication in the evolution of domain-domain interactions.PloS one · 2019Article
- Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins.Scientific reports · 2017Article
- Development of a motif-based topology-independent structure comparison method to identify evolutionarily related folds.Proteins · 2016Article
- Nonlinearities in protein space limit the utility of informatics in protein biophysics.Proteins · 2015Article
- Global view of the protein universe.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Conservation of protein structure over four billion years.Structure (London, England : 1993) · 2013Article
- A daily-updated tree of (sequenced) life as a reference for genome research.Scientific reports · 2013Article
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- Detection of spatial correlations in protein structures and molecular complexes.Structure (London, England : 1993) · 2012Article
- Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold.Computational biology and chemistry · 2011Article
- Generation of a consensus protein domain dictionary.Bioinformatics (Oxford, England) · 2011Article
- Protein folds and protein folding.Protein engineering, design & selection : PEDS · 2011Review
- 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
- The Mycobacterium tuberculosis drugome and its polypharmacological implications.PLoS computational biology · 2010Article
- Issues in bioinformatics benchmarking: the case study of multiple sequence alignment.Nucleic acids research · 2010Review
- Development of a novel bioinformatics tool for in silico validation of protein interactions.Journal of biomedicine & biotechnology · 2010Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
In this, the 200th anniversary of Charles Darwin's birth and the 150th anniversary of the publication of the Origin of Species, it is fitting to revisit the classification of protein structures from an evolutionary perspective. Existing classifications use homologous sequence relationships, but knowing that structure is much more conserved that sequence creates an iterative loop from which structures can be further classified beyond that of the domain, thereby teasing out distant evolutionary relationships. The desired classification scheme is then one in which a fold is merely semantics and structure can be classified as either ancestral or derived.
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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.