ArticleStructure (London, England : 1993)2009
Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.
Article in Structure (London, England : 1993), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- A comprehensive benchmarking of the AlphaFold3 for predicting biomacromolecules and their interactions.Briefings in bioinformatics · 2025Article
- AlphaFold2, SPINE-X, and Seder on Four Hard CASP Targets.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- 3 = 1 + 2: how the divide conquered de novo protein structure prediction and what is next?National science review · 2023Article
- Naive Prediction of Protein Backbone Phi and Psi Dihedral Angles Using Deep Learning.Molecules (Basel, Switzerland) · 2023Article
- Article
- A novel approach to analyze the association characteristics between post-spliced introns and their corresponding mRNA.Frontiers in genetics · 2023Article
- Deep learning for protein secondary structure prediction: Pre and post-AlphaFold.Computational and structural biotechnology journal · 2022Review
- A Hybrid Levenberg-Marquardt Algorithm on a Recursive Neural Network for Scoring Protein Models.Methods in molecular biology (Clifton, N.J.) · 2021Article
- PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids.Genes · 2020Article
- Enhancing protein backbone angle prediction by using simpler models of deep neural networks.Scientific reports · 2020Article
- RegSNPs-intron: a computational framework for predicting pathogenic impact of intronic single nucleotide variants.Genome biology · 2019Article
- Entropy, Fluctuations, and Disordered Proteins.Entropy (Basel, Switzerland) · 2019Article
- EvolStruct-Phogly: incorporating structural properties and evolutionary information from profile bigrams for the phosphoglycerylation prediction.BMC genomics · 2019Article
- PhoglyStruct: Prediction of phosphoglycerylated lysine residues using structural properties of amino acids.Scientific reports · 2018Article
- Refining protein structures using enhanced sampling techniques with restraints derived from an ensemble-based model.Protein science : a publication of the Protein Society · 2018Article
- Improving low-accuracy protein structures using enhanced sampling techniques.The Journal of chemical physics · 2018Article
- RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning.BMC bioinformatics · 2018Article
- Sequential search leads to faster, more efficient fragment-based de novo protein structure prediction.Bioinformatics (Oxford, England) · 2018Article
- Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures.BMC bioinformatics · 2018Article
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4 authors.
Funding
Abstract
Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g., three-state secondary structure). Here, we combine a two-state classifier with real-value predictor to predict local structure in continuous representation by backbone torsion angles. The accuracy of the angles predicted by this approach is close to that derived from NMR chemical shifts. Their substitution for predicted secondary structure as restraints for ab initio structure prediction doubles the success rate. This result demonstrates the potential of predicted local structure for fragment-free tertiary-structure prediction. It further implies potentially significant benefits from using predicted real-valued torsion angles as a replacement for or supplement to the secondary-structure prediction tools used almost exclusively in many computational methods ranging from sequence alignment to function prediction.
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