ArticleNucleic acids research2025
CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Multi-tope subunit vaccine for human anthrax through pan-genome-based reverse vaccinology approach.Molecular genetics and genomics : MGG · 2026Article
- Allosteric regulation of fibronectin binding by the anti-β1 integrin antibody TS2/16.PNAS nexus · 2026Article
- Computational identification of rare pathogenic genomic variants in esophageal cancer markers: Transcript-level analysis, sequence-based insights, and structural-functional impacts of non-synonymous SNPs.Biochemistry and biophysics reports · 2026Article
- AGGRESCAN and its evolution: A two-decade perspective on protein aggregation prediction.Biophysical reviews · 2026Review
- Dormancy Versus Germination: 3D Protein Modeling and Evolutionary Analyses Define the Roles of Genetic Variants in the Barley MKK3 Enzyme.International journal of molecular sciences · 2026Article
- Structural and Computational Insights into the Attenuated Innate Immune Recognition of the SARS-CoV-2 N15 Lineage, an Early-Pandemic Variant.Computational and structural biotechnology journal · 2026Article
- Antiplasmodial Activity of Methylangolensate FromJournal of tropical medicine · 2026Article
- Antagonist Binding Actively Disrupts Interleukin-1 Receptor Dynamics to Block Co-receptor Recruitment.Computational and structural biotechnology journal · 2026Article
- Development and Immunogenicity Assessment of a Multi-Epitope Antigen Against Zika Virus: An In Silico and In Vivo Approach.Vaccines · 2025Article
- Design of a Multi-Epitope Vaccine using β-barrel Outer Membrane Proteins Identified in Chlamydia trachomatis.The Journal of membrane biology · 2025Article
- The Paulinella chromatophore transit peptide part2 adopts a structural fold similar to the γ-glutamyl-cyclotransferase fold.Plant physiology · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Simulating protein structure flexibility using classical methods is computationally demanding, especially for large proteins. To address this challenge, we have been developing the CABS-flex method, which enables fast simulations of protein structural flexibility by combining a coarse-grained simulation approach with all-atom detail. Previously available as the CABS-flex 2.0 web server, the method has now undergone a major upgrade with the release of CABS-flex 3.0. Key improvements include the introduction of intuitive flexibility modes that simplify the control of distance restraints and allow users to reflect known or expected dynamic regions; improved all-atom reconstruction for higher-quality model generation; a new feature for de novo peptide structure prediction, supporting both linear and cyclic peptides along with their conformational flexibility; and new tools for result analysis and visualization, facilitating deeper insights into structural flexibility. Additionally, AlphaFold pLDDT-derived restraints can be used as optional input for guiding simulations. The method accepts input as either a PDB/mmCIF structure or a sequence (for peptide modeling). Advanced options allow users to incorporate experimental or computational restraints. The CABS-flex 3.0 web server is available at https://lcbio.pl/cabsflex3. This website is free and open to all users, with no login requirement.
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Registered trials
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