ArticleProteomics2011
Protein 8-class secondary structure prediction using conditional neural fields.
Article in Proteomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
- Intrinsically disordered regions facilitate Mlp1-Nab2 recognition in mRNA quality control.Nucleus (Austin, Tex.) · 2026Article
- Sculpting conducting nanopore size and shape through de novo protein design.Science (New York, N.Y.) · 2024Article
- ProteinMPNN Recovers Complex Sequence Properties of Transmembrane β-barrels.bioRxiv : the preprint server for biology · 2024Article
- Sculpting conducting nanopore size and shape throughbioRxiv : the preprint server for biology · 2023Article
- Naive Prediction of Protein Backbone Phi and Psi Dihedral Angles Using Deep Learning.Molecules (Basel, Switzerland) · 2023Article
- BIAPSS: A Comprehensive Physicochemical Analyzer of Proteins Undergoing Liquid-Liquid Phase Separation.International journal of molecular sciences · 2022Article
- Genotypic, proteomic, and phenotypic approaches to decipher the response to caspofungin and calcineurin inhibitors in clinical isolates of echinocandin-resistant Candida glabrata.The Journal of antimicrobial chemotherapy · 2022Article
- Designing of peptide aptamer targeting the receptor-binding domain of spike protein of SARS-CoV-2: an in silico study.Molecular diversity · 2022Article
- A tale of solving two computational challenges in protein science: neoantigen prediction and protein structure prediction.Briefings in bioinformatics · 2022Review
- Proteomic Tools for the Analysis of Cytoskeleton Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Prediction of protein secondary structure based on an improved channel attention and multiscale convolution module.Frontiers in bioengineering and biotechnology · 2022Article
- Discovering the Ultimate Limits of Protein Secondary Structure Prediction.Biomolecules · 2021Article
- CheSPI: chemical shift secondary structure population inference.Journal of biomolecular NMR · 2021Article
- A secondary structure-based position-specific scoring matrix applied to the improvement in protein secondary structure prediction.PloS one · 2021Article
- The influence of dataset homology and a rigorous evaluation strategy on protein secondary structure prediction.PloS one · 2021Article
- Extracellular loops matter - subcellular location and function of the lysine transporter Lyp1 from Saccharomyces cerevisiae.The FEBS journal · 2020Article
- A simple strategy to enhance the speed of protein secondary structure prediction without sacrificing accuracy.PloS one · 2020Article
- DeepACLSTM: deep asymmetric convolutional long short-term memory neural models for protein secondary structure prediction.BMC bioinformatics · 2019Article
- PiPred - a deep-learning method for prediction of π-helices in protein sequences.Scientific reports · 2019Article
- CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis.Genome biology · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Compared with the protein 3-class secondary structure (SS) prediction, the 8-class prediction gains less attention and is also much more challenging, especially for proteins with few sequence homologs. This paper presents a new probabilistic method for 8-class SS prediction using conditional neural fields (CNFs), a recently invented probabilistic graphical model. This CNF method not only models the complex relationship between sequence features and SS, but also exploits the interdependency among SS types of adjacent residues. In addition to sequence profiles, our method also makes use of non-evolutionary information for SS prediction. Tested on the CB513 and RS126 data sets, our method achieves Q8 accuracy of 64.9 and 64.7%, respectively, which are much better than the SSpro8 web server (51.0 and 48.0%, respectively). Our method can also be used to predict other structure properties (e.g. solvent accessibility) of a protein or the SS of RNA.
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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.