ArticleNucleic acids research2012
PredyFlexy: flexibility and local structure prediction from sequence.
Article in Nucleic acids research, 2012. 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.
- PEGASUS: Prediction of MD-derived protein flexibility from sequence.Protein science : a publication of the Protein Society · 2025Article
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- Impact of SARS-CoV-2 Variant NSP6 on Pathogenicity: Genetic Analysis and Cell Biology.Current issues in molecular biology · 2025Article
- Persistent Sheaf Laplacian Analysis of Protein Flexibility.The journal of physical chemistry. B · 2025Article
- Multiscale Differential Geometry Learning for Protein Flexibility Analysis.Journal of computational chemistry · 2025Article
- Enhanced thermostability of nattokinase by rational design of disulfide bond.Microbial cell factories · 2025Article
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- Machine Learning Models to Interrogate Proteome-Wide Covalent Ligandabilities Directed at Cysteines.JACS Au · 2024Article
- Case report: A severe clinical phenotype of pontocerebellar hypoplasia type 7 with compound heterozygous variants of TOE1.Heliyon · 2024Article
- Machine Learning Models to Interrogate Proteomewide Covalent Ligandabilities Directed at Cysteines.bioRxiv : the preprint server for biology · 2024Article
- General Trends of theInternational journal of molecular sciences · 2023Article
- Analysis of Integrin αInternational journal of molecular sciences · 2022Article
- An in-silico study of the mutation-associated effects on the spike protein of SARS-CoV-2, Omicron variant.PloS one · 2022Article
- PSSMCOOL: a comprehensive R package for generating evolutionary-based descriptors of protein sequences from PSSM profiles.Biology methods & protocols · 2022Article
- PYTHIA: Deep Learning Approach for Local Protein Conformation Prediction.International journal of molecular sciences · 2021Article
- b2bTools: online predictions for protein biophysical features and their conservation.Nucleic acids research · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- A hijack mechanism of Indian SARS-CoV-2 isolates for relapsing contemporary antiviral therapeutics.Computers in biology and medicine · 2021Article
- Computational Analysis of Missense Variants in the Human Transmembrane Protease Serine 2 (BioMed research international · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein structures are necessary for understanding protein function at a molecular level. Dynamics and flexibility of protein structures are also key elements of protein function. So, we have proposed to look at protein flexibility using novel methods: (i) using a structural alphabet and (ii) combining classical X-ray B-factor data and molecular dynamics simulations. First, we established a library composed of structural prototypes (LSPs) to describe protein structure by a limited set of recurring local structures. We developed a prediction method that proposes structural candidates in terms of LSPs and predict protein flexibility along a given sequence. Second, we examine flexibility according to two different descriptors: X-ray B-factors considered as good indicators of flexibility and the root mean square fluctuations, based on molecular dynamics simulations. We then define three flexibility classes and propose a method based on the LSP prediction method for predicting flexibility along the sequence. This method does not resort to sophisticate learning of flexibility but predicts flexibility from average flexibility of predicted local structures. The method is implemented in PredyFlexy web server. Results are similar to those obtained with the most recent, cutting-edge methods based on direct learning of flexibility data conducted with sophisticated algorithms. PredyFlexy can be accessed at http://www.dsimb.inserm.fr/dsimb_tools/predyflexy/.
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