ArticleBriefings in bioinformatics2024
Structure prediction of linear and cyclic peptides using CABS-flex.
Article in Briefings in bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- HighRes_Builder: improved access and modeling of noncanonical residues for protein structure prediction.Briefings in bioinformatics · 2026Article
- Flexible Docking of Cyclic Peptides to Proteins Using CABS-dock.Journal of chemical theory and computation · 2025Article
- Accurate structure prediction of cyclic peptides containing unnatural amino acids using HighFold3.Briefings in bioinformatics · 2025Article
- Structural and functional analysis of the accessory gene regulators of Staphylococcus aureus and Staphylococcus epidermidis: an in Silico approach.BMC microbiology · 2025Article
- CABS-flex 3.0: an online tool for simulating protein structural flexibility and peptide modeling.Nucleic acids research · 2025Article
- Structural information in therapeutic peptides: Emerging applications in biomedicine.FEBS open bio · 2025Review
- Insight into Protein Engineering: FromCurrent pharmaceutical design · 2025Review
- Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations.Computational and structural biotechnology journal · 2024Article
- Exploring protein functions from structural flexibility using CABS-flex modeling.Protein science : a publication of the Protein Society · 2024Review
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
The structural modeling of peptides can be a useful aid in the discovery of new drugs and a deeper understanding of the molecular mechanisms of life. Here we present a novel multiscale protocol for the structure prediction of linear and cyclic peptides. The protocol combines two main stages: coarse-grained simulations using the CABS-flex standalone package and an all-atom reconstruction-optimization process using the Modeller program. We evaluated the protocol on a set of linear peptides and two sets of cyclic peptides, with cyclization through the backbone and disulfide bonds. A comparison with other state-of-the-art tools (APPTEST, PEP-FOLD, ESMFold and AlphaFold implementation in ColabFold) shows that for most cases, AlphaFold offers the highest resolution. However, CABS-flex is competitive, particularly when it comes to short linear peptides. As demonstrated, the protocol performance can be further improved by combination with the residue-residue contact prediction method or more efficient scoring. The protocol is included in the CABS-flex standalone package along with online documentation to aid users in predicting the structure of peptides and mini-proteins.
Indexed as
Identifiers
What OpenQuestion holds
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.