ArticleProtein science : a publication of the Protein Society2020
Computational design of mixed chirality peptide macrocycles with internal symmetry.
Article in Protein science : a publication of the Protein Society, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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
20 citing papers in PubMed, 35 citations in OpenAlex.
- HighFold-MeD: a Rosetta distillation model to accelerate structure prediction of cyclic peptides with backbone N-methylation and D-amino acids.Journal of cheminformatics · 2025Article
- The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design.bioRxiv : the preprint server for biology · 2025Article
- Robust Conformational Space Exploration of Cyclic Peptides by Combining Different MD Protocols and Force Fields.Journal of chemical theory and computation · 2025Article
- Heuristic energy-based cyclic peptide design.PLoS computational biology · 2025Article
- Heuristic energy-based cyclic peptide design.bioRxiv : the preprint server for biology · 2025Article
- CYCLICCAE: A CONFORMATIONAL AUTOENCODER FOR EFFICIENT HETEROCHIRAL MACROCYCLIC BACKBONE SAMPLING.bioRxiv : the preprint server for biology · 2025Article
- Parameterizing non-canonical amino acids for cyclic peptide simulations.Methods in enzymology · 2025Article
- Artificial Intelligence Transforming Post-Translational Modification Research.Bioengineering (Basel, Switzerland) · 2024Review
- Accurate de novo design of heterochiral protein-protein interactions.Cell research · 2024Article
- Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics.Chemical reviews · 2024Review
- FMOe: Preprocessing and Visualizing Package of the Fragment Molecular Orbital Method for Molecular Operating Environment and Its Applications in Covalent Ligand and Metalloprotein Analyses.Journal of chemical information and modeling · 2024Article
- Sparks of function by de novo protein design.Nature biotechnology · 2024Review
- Design of stimulus-responsive two-state hinge proteins.Science (New York, N.Y.) · 2023Article
- Cell-permeable chameleonic peptides: Exploiting conformational dynamics in de novo cyclic peptide design.Current opinion in structural biology · 2023Review
- Exploration of Structured Symmetric Cyclic Peptides as Ligands for Metal-Organic Frameworks.Chemistry of materials : a publication of the American Chemical Society · 2022Article
- Computational Site Saturation Mutagenesis of Canonical and Non-Canonical Amino Acids to Probe Protein-Peptide Interactions.Frontiers in molecular biosciences · 2022Article
- Computational Design of Structured and Functional Peptide Macrocycles.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A mixed chirality α-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography.RSC chemical biology · 2021Article
- Computationally designed peptide macrocycle inhibitors of New Delhi metallo-β-lactamase 1.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Computational design of mixed chirality peptide macrocycles with internal symmetry.Protein science : a publication of the Protein Society · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
Cyclic symmetry is frequent in protein and peptide homo-oligomers, but extremely rare within a single chain, as it is not compatible with free N- and C-termini. Here we describe the computational design of mixed-chirality peptide macrocycles with rigid structures that feature internal cyclic symmetries or improper rotational symmetries inaccessible to natural proteins. Crystal structures of three C2- and C3-symmetric macrocycles, and of six diverse S2-symmetric macrocycles, match the computationally-designed models with backbone heavy-atom RMSD values of 1 Å or better. Crystal structures of an S4-symmetric macrocycle (consisting of a sequence and structure segment mirrored at each of three successive repeats) designed to bind zinc reveal a large-scale zinc-driven conformational change from an S4-symmetric apo-state to a nearly inverted S4-symmetric holo-state almost identical to the design model. These symmetric structures provide promising starting points for applications ranging from design of cyclic peptide based metal organic frameworks to creation of high affinity binders of symmetric protein homo-oligomers. More generally, this work demonstrates the power of computational design for exploring symmetries and structures not found in nature, and for creating synthetic switchable systems.
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.