ArticleProtein science : a publication of the Protein Society2002
Rapid protein domain assignment from amino acid sequence using predicted secondary structure.
Article in Protein science : a publication of the Protein Society, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed.
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- Res-Dom: predicting protein domain boundary from sequence using deep residual network and Bi-LSTM.Bioinformatics advances · 2022Article
- Modeling the Tertiary Structure of the Rift Valley Fever Virus L Protein.Molecules (Basel, Switzerland) · 2019Article
- The Vaccinia virion: Filling the gap between atomic and ultrastructure.PLoS pathogens · 2019Article
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- Combining Wet and Dry Lab Techniques to Guide the Crystallization of Large Coiled-coil Containing Proteins.Journal of visualized experiments : JoVE · 2017Article
- Protein crystallization: Eluding the bottleneck of X-ray crystallography.AIMS biophysics · 2017Article
- Biochemical characterization of PE_PGRS61 family protein ofIranian journal of basic medical sciences · 2016Article
- PAT: predictor for structured units and its application for the optimization of target molecules for the generation of synthetic antibodies.BMC bioinformatics · 2016Article
- Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement.Frontiers in physiology · 2016Article
- Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer.The Journal of biological chemistry · 2015Article
- Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.Molecular & cellular proteomics : MCP · 2014Article
- Dynactin integrity depends upon direct binding of dynamitin to Arp1.Molecular biology of the cell · 2014Article
- Protein inter-domain linker prediction using Random Forest and amino acid physiochemical properties.BMC bioinformatics · 2014Article
- Comprehensive repertoire of foldable regions within whole genomes.PLoS computational biology · 2013Article
- A novel automethylation reaction in the Aspergillus nidulans LaeA protein generates S-methylmethionine.The Journal of biological chemistry · 2013Article
- Article
- DomHR: accurately identifying domain boundaries in proteins using a hinge region strategy.PloS one · 2013Article
- Functional dissection of the multi-domain di-heme cytochrome c(550) from Thermus thermophilus.PloS one · 2013Article
- Cloning and characterization of rainbow trout interleukin-17A/F2 (IL-17A/F2) and IL-17 receptor A: expression during infection and bioactivity of recombinant IL-17A/F2.Infection and immunity · 2013Article
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3 authors.
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Abstract
The elucidation of the domain content of a given protein sequence in the absence of determined structure or significant sequence homology to known domains is an important problem in structural biology. Here we address how successfully the delineation of continuous domains can be accomplished in the absence of sequence homology using simple baseline methods, an existing prediction algorithm (Domain Guess by Size), and a newly developed method (DomSSEA). The study was undertaken with a view to measuring the usefulness of these prediction methods in terms of their application to fully automatic domain assignment. Thus, the sensitivity of each domain assignment method was measured by calculating the number of correctly assigned top scoring predictions. We have implemented a new continuous domain identification method using the alignment of predicted secondary structures of target sequences against observed secondary structures of chains with known domain boundaries as assigned by Class Architecture Topology Homology (CATH). Taking top predictions only, the success rate of the method in correctly assigning domain number to the representative chain set is 73.3%. The top prediction for domain number and location of domain boundaries was correct for 24% of the multidomain set (+/-20 residues). These results have been put into context in relation to the results obtained from the other prediction methods assessed.
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