ArticleBioinformatics (Oxford, England)2007
Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM).
Article in Bioinformatics (Oxford, England), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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
11 citing papers in PubMed.
- COMTOP: Protein Residue-Residue Contact Prediction through Mixed Integer Linear Optimization.Membranes · 2021Article
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in bioinformatics · 2018Article
- Knowledge-based prediction of protein backbone conformation using a structural alphabet.PloS one · 2017Article
- Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.Scientific reports · 2015Article
- From local structure to a global framework: recognition of protein folds.Journal of the Royal Society, Interface · 2014Review
- Distributions of amino acids suggest that certain residue types more effectively determine protein secondary structure.Journal of molecular modeling · 2013Article
- Platelet adhesion to decorin but not collagen I correlates with the integrin α2 dimorphism E534K, the basis of the human platelet alloantigen (HPA)-5 system.Haematologica · 2012Article
- SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles.Journal of computational chemistry · 2012Article
- Evolutionary history of tissue kallikreins.PloS one · 2010Article
- Template-based protein modeling: recent methodological advances.Current topics in medicinal chemistry · 2010Review
- A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.PLoS genetics · 2009Article
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Authors and funding
4 authors.
Funding
Abstract
One of the challenges in protein secondary structure prediction is to overcome the cross-validated 80% prediction accuracy barrier. Here, we propose a novel approach to surpass this barrier. Instead of using a single algorithm that relies on a limited data set for training, we combine two complementary methods having different strengths: Fragment Database Mining (FDM) and GOR V. FDM harnesses the availability of the known protein structures in the Protein Data Bank and provides highly accurate secondary structure predictions when sequentially similar structural fragments are identified. In contrast, the GOR V algorithm is based on information theory, Bayesian statistics, and PSI-BLAST multiple sequence alignments to predict the secondary structure of residues inside a sliding window along a protein chain. A combination of these two different methods benefits from the large number of structures in the PDB and significantly improves the secondary structure prediction accuracy, resulting in Q3 ranging from 67.5 to 93.2%, depending on the availability of highly similar fragments in the Protein Data Bank.
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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.