ArticleGenome research2011
The Proteome Folding Project: proteome-scale prediction of structure and function.
Article in Genome research, 2011. 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-folding chaperones predict structure-function relationships and cancer risk in BRCA1 mutation carriers.Cell reports · 2024Article
- Oral Mucosa in Cancer Patients-Putting the Pieces Together: A Narrative Review and New Perspectives.Cancers · 2023Review
- Development of anti-PD-L1 antibody based on structure prediction of AlphaFold2.Frontiers in immunology · 2023Article
- Article
- A Single-Organelle Optical Omics Platform for Cell Science and Biomarker Discovery.Analytical chemistry · 2021Article
- Better together: Elements of successful scientific software development in a distributed collaborative community.PLoS computational biology · 2020Review
- Article
- Homology modeling in a dynamical world.Protein science : a publication of the Protein Society · 2017Article
- Complete fold annotation of the human proteome using a novel structural feature space.Scientific reports · 2017Article
- Evolution and structural diversification of Nictaba-like lectin genes in food crops with a focus on soybean (Glycine max).Annals of botany · 2017Article
- Improving protein complex prediction by reconstructing a high-confidence protein-protein interaction network of Escherichia coli from different physical interaction data sources.BMC bioinformatics · 2017Article
- Effects of ADAMTS14 genetic polymorphism and cigarette smoking on the clinicopathologic development of hepatocellular carcinoma.PloS one · 2017Article
- Use of a structural alphabet to find compatible folds for amino acid sequences.Protein science : a publication of the Protein Society · 2015Article
- From local structure to a global framework: recognition of protein folds.Journal of the Royal Society, Interface · 2014Review
- Proteome folding kinetics is limited by protein halflife.PloS one · 2014Article
- Structure prediction and analysis of DNA transposon and LINE retrotransposon proteins.The Journal of biological chemistry · 2013Article
- Parametric Bayesian priors and better choice of negative examples improve protein function prediction.Bioinformatics (Oxford, England) · 2013Article
- Tertiary model of a plant cellulose synthase.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- A domain-centric solution to functional genomics via dcGO Predictor.BMC bioinformatics · 2013Article
- One stop shop for everything Dictyostelium: dictyBase and the Dicty Stock Center in 2012.Methods in molecular biology (Clifton, N.J.) · 2013Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
The incompleteness of proteome structure and function annotation is a critical problem for biologists and, in particular, severely limits interpretation of high-throughput and next-generation experiments. We have developed a proteome annotation pipeline based on structure prediction, where function and structure annotations are generated using an integration of sequence comparison, fold recognition, and grid-computing-enabled de novo structure prediction. We predict protein domain boundaries and three-dimensional (3D) structures for protein domains from 94 genomes (including human, Arabidopsis, rice, mouse, fly, yeast, Escherichia coli, and worm). De novo structure predictions were distributed on a grid of more than 1.5 million CPUs worldwide (World Community Grid). We generated significant numbers of new confident fold annotations (9% of domains that are otherwise unannotated in these genomes). We demonstrate that predicted structures can be combined with annotations from the Gene Ontology database to predict new and more specific molecular functions.
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What OpenQuestion holds
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.