ReviewCurrent opinion in structural biology2012
The use of evolutionary patterns in protein annotation.
Review in Current opinion in structural biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed.
- Integrating evidence from protein domains to identify cancer driver mutations.Protein science : a publication of the Protein Society · 2026Article
- Odd one out? Functional tuning of Zymomonas mobilis pyruvate kinase is narrower than its allosteric, human counterpart.Protein science : a publication of the Protein Society · 2022Article
- Inter-paralog amino acid inversion events in large phylogenies of duplicated proteins.PLoS computational biology · 2022Article
- Recurrent high-impact mutations at cognate structural positions in class A G protein-coupled receptors expressed in tumors.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Recent Applications of Deep Learning Methods on Evolution- and Contact-Based Protein Structure Prediction.International journal of molecular sciences · 2021Review
- Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer.Cancer cell · 2020Article
- 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns.International journal of molecular sciences · 2019Article
- Harnessing Marine Biocatalytic Reservoirs for Green Chemistry Applications through Metagenomic Technologies.Marine drugs · 2018Review
- Evolutionary action and structural basis of the allosteric switch controlling βNature communications · 2017Article
- CorNet: Assigning function to networks of co-evolving residues by automated literature mining.PloS one · 2017Article
- Article
- Computational approaches for classification and prediction of P-type ATPase substrate specificity in Arabidopsis.Physiology and molecular biology of plants : an international journal of functional plant biology · 2016Article
- Article
- Biochemical functional predictions for protein structures of unknown or uncertain function.Computational and structural biotechnology journal · 2015Review
- The functional importance of co-evolving residues in proteins.Cellular and molecular life sciences : CMLS · 2014Review
- Prediction and experimental validation of enzyme substrate specificity in protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- FFPred 2.0: improved homology-independent prediction of gene ontology terms for eukaryotic protein sequences.PloS one · 2013Article
- Article
- Structure-based function prediction of uncharacterized protein using binding sites comparison.PLoS computational biology · 2013Article
- Prediction and redesign of protein-protein interactions.Progress in biophysics and molecular biologyReview
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
With genomic data skyrocketing, their biological interpretation remains a serious challenge. Diverse computational methods address this problem by pointing to the existence of recurrent patterns among sequence, structure, and function. These patterns emerge naturally from evolutionary variation, natural selection, and divergence--the defining features of biological systems--and they identify molecular events and shapes that underlie specificity of function and allosteric communication. Here we review these methods, and the patterns they identify in case studies and in proteome-wide applications, to infer and rationally redesign function.
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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.