ArticleNucleic acids research2004
Sequence-based prediction of protein domains.
Article in Nucleic acids research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Embeddings from protein language models predict conservation and variant effects.Human genetics · 2022Article
- Protein domain identification methods and online resources.Computational and structural biotechnology journal · 2021Review
- ThreaDomEx: a unified platform for predicting continuous and discontinuous protein domains by multiple-threading and segment assembly.Nucleic acids research · 2017Article
- PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.Journal of molecular modeling · 2016Article
- Solution structure of a soluble fragment derived from a membrane protein by shotgun proteolysis.Protein engineering, design & selection : PEDS · 2015Article
- Article
- DomHR: accurately identifying domain boundaries in proteins using a hinge region strategy.PloS one · 2013Article
- The MULTICOM toolbox for protein structure prediction.BMC bioinformatics · 2012Article
- Article
- DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning.BMC bioinformatics · 2011Article
- Practical application of bioinformatics by the multidisciplinary VIZIER consortium.Antiviral research · 2010Review
- DomSVR: domain boundary prediction with support vector regression from sequence information alone.Amino acids · 2010Article
- Article
- Sequence and structural analysis of 4SNc-Tudor domain protein from Takifugu Rubripes.Bioinformation · 2009Article
- Ab initio and homology based prediction of protein domains by recursive neural networks.BMC bioinformatics · 2009Article
- Folding by numbers: primary sequence statistics and their use in studying protein folding.International journal of molecular sciences · 2009Review
- OPUS-Dom: applying the folding-based method VECFOLD to determine protein domain boundaries.Journal of molecular biology · 2009Article
- Protein domain boundary predictions: a structural biology perspective.The open biochemistry journal · 2009Article
- SiteSeek: post-translational modification analysis using adaptive locality-effective kernel methods and new profiles.BMC bioinformatics · 2008Article
- Identifying foldable regions in protein sequence from the hydrophobic signal.Nucleic acids research · 2008Article
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2 authors.
Funding
Abstract
Guessing the boundaries of structural domains has been an important and challenging problem in experimental and computational structural biology. Predictions were based on intuition, biochemical properties, statistics, sequence homology and other aspects of predicted protein structure. Here, we introduced CHOPnet, a de novo method that predicts structural domains in the absence of homology to known domains. Our method was based on neural networks and relied exclusively on information available for all proteins. Evaluating sustained performance through rigorous cross-validation on proteins of known structure, we correctly predicted the number of domains in 69% of all proteins. For 50% of the two-domain proteins the centre of the predicted boundary was closer than 20 residues to the boundary assigned from three-dimensional (3D) structures; this was about eight percentage points better than predictions by 'equal split'. Our results appeared to compare favourably with those from previously published methods. CHOPnet may be useful to restrict the experimental testing of different fragments for structure determination in the context of structural genomics.
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