ArticlePloS one2013
Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Applications and limitations of AI tools in enzyme design.Protein science : a publication of the Protein Society · 2026Review
- Topological deep learning for enhancing peptide-protein complex prediction.Communications chemistry · 2025Article
- The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design.bioRxiv : the preprint server for biology · 2025Article
- Computational Design of Lysine Targeting Covalent Binders Using Rosetta.Journal of chemical information and modeling · 2025Article
- Article
- Automated Engineering Protein Dynamics via Loop Grafting: ImprovingACS catalysis · 2025Article
- Artificial Intelligence Transforming Post-Translational Modification Research.Bioengineering (Basel, Switzerland) · 2024Review
- Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds.Proteins · 2024Article
- Design of target specific peptide inhibitors using generative deep learning and molecular dynamics simulations.Nature communications · 2024Article
- A simple method for developing lysine targeted covalent protein reagents.Nature communications · 2023Article
- Protocol for iterative optimization of modified peptides bound to protein targets.Journal of computer-aided molecular design · 2022Article
- Computational Site Saturation Mutagenesis of Canonical and Non-Canonical Amino Acids to Probe Protein-Peptide Interactions.Frontiers in molecular biosciences · 2022Article
- Covalent flexible peptide docking in Rosetta.Chemical science · 2021Article
- Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution.Journal of chemical information and modeling · 2021Article
- Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.Biochemistry · 2021Review
- Piptides: New, Easily Accessible Chemotypes For Interactions With Biomolecules.Angewandte Chemie (International ed. in English) · 2021Article
- Modulating Protein-Protein Interactions by Cyclic and Macrocyclic Peptides. Prominent Strategies and Examples.Molecules (Basel, Switzerland) · 2021Review
- A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics.The Journal of chemical physics · 2020Article
- In-solution enrichment identifies peptide inhibitors of protein-protein interactions.Nature chemical biology · 2019Article
- Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer.Nature communications · 2018Article
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Authors and funding
19 authors.
Funding
Abstract
Peptidomimetics are classes of molecules that mimic structural and functional attributes of polypeptides. Peptidomimetic oligomers can frequently be synthesized using efficient solid phase synthesis procedures similar to peptide synthesis. Conformationally ordered peptidomimetic oligomers are finding broad applications for molecular recognition and for inhibiting protein-protein interactions. One critical limitation is the limited set of design tools for identifying oligomer sequences that can adopt desired conformations. Here, we present expansions to the ROSETTA platform that enable structure prediction and design of five non-peptidic oligomer scaffolds (noncanonical backbones), oligooxopiperazines, oligo-peptoids, [Formula: see text]-peptides, hydrogen bond surrogate helices and oligosaccharides. This work is complementary to prior additions to model noncanonical protein side chains in ROSETTA. The main purpose of our manuscript is to give a detailed description to current and future developers of how each of these noncanonical backbones was implemented. Furthermore, we provide a general outline for implementation of new backbone types not discussed here. To illustrate the utility of this approach, we describe the first tests of the ROSETTA molecular mechanics energy function in the context of oligooxopiperazines, using quantum mechanical calculations as comparison points, scanning through backbone and side chain torsion angles for a model peptidomimetic. Finally, as an example of a novel design application, we describe the automated design of an oligooxopiperazine that inhibits the p53-MDM2 protein-protein interaction. For the general biological and bioengineering community, several noncanonical backbones have been incorporated into web applications that allow users to freely and rapidly test the presented protocols (http://rosie.rosettacommons.org). This work helps address the peptidomimetic community's need for an automated and expandable modeling tool for noncanonical backbones.
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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.