ArticleProteins2009
A new prediction strategy for long local protein structures using an original description.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- AlphaFold modeling uncovers global structural features of class I and class II fungal hydrophobins.Protein science : a publication of the Protein Society · 2025Article
- Evaluation of the Potential Impact of In Silico Humanization on VInternational journal of molecular sciences · 2023Article
- General Trends of theInternational journal of molecular sciences · 2023Article
- Oxa-376 and Oxa-530 variants of β-lactamase: computational study uncovers potential therapeutic targets ofRSC advances · 2022Article
- In silico analysis of Glanzmann variants of Calf-1 domain of αScientific reports · 2017Article
- Protein flexibility in the light of structural alphabets.Frontiers in molecular biosciences · 2015Review
- From local structure to a global framework: recognition of protein folds.Journal of the Royal Society, Interface · 2014Review
- A novel approach to represent and compare RNA secondary structures.Nucleic acids research · 2014Article
- PredyFlexy: flexibility and local structure prediction from sequence.Nucleic acids research · 2012Article
- Article
- BriX: a database of protein building blocks for structural analysis, modeling and design.Nucleic acids research · 2011Article
- A short survey on protein blocks.Biophysical reviews · 2010Article
- Analysis of loop boundaries using different local structure assignment methods.Protein science : a publication of the Protein Society · 2009Article
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3 authors.
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Abstract
A relevant and accurate description of three-dimensional (3D) protein structures can be achieved by characterizing recurrent local structures. In a previous study, we developed a library of 120 3D structural prototypes encompassing all known 11-residues long local protein structures and ensuring a good quality of structural approximation. A local structure prediction method was also proposed. Here, overlapping properties of local protein structures in global ones are taken into account to characterize frequent local networks. At the same time, we propose a new long local structure prediction strategy which involves the use of evolutionary information coupled with Support Vector Machines (SVMs). Our prediction is evaluated by a stringent geometrical assessment. Every local structure prediction with a Calpha RMSD less than 2.5 A from the true local structure is considered as correct. A global prediction rate of 63.1% is then reached, corresponding to an improvement of 7.7 points compared with the previous strategy. In the same way, the prediction of 88.33% of the 120 structural classes is improved with 8.65% mean gain. 85.33% of proteins have better prediction results with a 9.43% average gain. An analysis of prediction rate per local network also supports the global improvement and gives insights into the potential of our method for predicting super local structures. Moreover, a confidence index for the direct estimation of prediction quality is proposed. Finally, our method is proved to be very competitive with cutting-edge strategies encompassing three categories of local structure predictions.
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