ArticleBioinformatics (Oxford, England)2014
CABS-flex predictions of protein flexibility compared with NMR ensembles.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
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- Novel genetic variants identification and immune profiling in ataxia telangiectasia patients.Journal of translational medicine · 2026Article
- Pangenome-based network analysis of Acinetobacter baumannii reveals the landscape of conserved therapeutic targets.Molecular diversity · 2026Article
- Antagonist Binding Actively Disrupts Interleukin-1 Receptor Dynamics to Block Co-receptor Recruitment.Computational and structural biotechnology journal · 2026Article
- CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling.Nucleic acids research · 2025Article
- Importance of Secondary Structure Data in Large Scale Protein Modeling Using Low-Resolution SURPASS Method.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations.Computational and structural biotechnology journal · 2024Article
- Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity.Protein science : a publication of the Protein Society · 2024Review
- Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution.Journal of chemical theory and computation · 2024Article
- Exploring protein functions from structural flexibility using CABS-flex modeling.Protein science : a publication of the Protein Society · 2024Review
- Exploring the nuclear proteins, viral capsid protein, and early antigen protein using immunoinformatic and molecular modeling approaches to design a vaccine candidate against Epstein Barr virus.Scientific reports · 2024Article
- Structure prediction of linear and cyclic peptides using CABS-flex.Briefings in bioinformatics · 2024Article
- Potential Antidiabetic Activity of β-sitosterol fromCombinatorial chemistry & high throughput screening · 2024Article
- Molecular docking-based virtual screening, drug-likeness, and pharmacokinetic profiling of some anti-Journal of Taibah University Medical Sciences · 2023Article
- Understanding the Molecular Regulation of Serotonin Receptor 5-HTRJournal of molecular neuroscience : MN · 2023Article
- Integrative modeling of diverse protein-peptide systems using CABS-dock.PLoS computational biology · 2023Article
- Membrane Cholesterol Inhibits Progesterone-Mediated Sperm Function through the Possible Involvement of ABHD2.International journal of molecular sciences · 2023Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationIdentification of flexible regions of protein structures is important for understanding of their biological functions. Recently, we have developed a fast approach for predicting protein structure fluctuations from a single protein model: the CABS-flex. CABS-flex was shown to be an efficient alternative to conventional all-atom molecular dynamics (MD). In this work, we evaluate CABS-flex and MD predictions by comparison with protein structural variations within NMR ensembles.
resultsBased on a benchmark set of 140 proteins, we show that the relative fluctuations of protein residues obtained from CABS-flex are well correlated to those of NMR ensembles. On average, this correlation is stronger than that between MD and NMR ensembles. In conclusion, CABS-flex is useful and complementary to MD in predicting protein regions that undergo conformational changes as well as the extent of such changes. AVAILABILITY AND IMPLEMENTATION: The CABS-flex is freely available to all users at http://biocomp.chem.uw.edu.pl/CABSflex. CONTACT: sekmi@chem.uw.edu.pl SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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