ArticleJournal of the American Chemical Society2014
A rotamer library to enable modeling and design of peptoid foldamers.
Article in Journal of the American Chemical Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- Artificial Intelligence Transforming Post-Translational Modification Research.Bioengineering (Basel, Switzerland) · 2024Review
- Article
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
- From Collagen Mimetics to Collagen Hybridization and Back.Accounts of chemical research · 2024Article
- Article
- Invariant point message passing for protein side chain packing.bioRxiv : the preprint server for biology · 2023Article
- An end-to-end deep learning method for protein side-chain packing and inverse folding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations.Protein science : a publication of the Protein Society · 2022Article
- Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.The journal of physical chemistry. B · 2022Article
- Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations.Macromolecules · 2022Article
- Computational Design of Structured and Functional Peptide Macrocycles.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Peptoid-based reprogrammable template for cell-permeable inhibitors of protein-protein interactions.Chemical science · 2021Article
- Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution.Journal of chemical information and modeling · 2021Article
- Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We?Frontiers in molecular biosciences · 2020Review
- Design of Peptoid-peptide Macrocycles to Inhibit the β-catenin TCF Interaction in Prostate Cancer.Nature communications · 2018Article
- Molecular dynamics-derived rotamer libraries for d-amino acids within homochiral and heterochiral polypeptides.Protein engineering, design & selection : PEDS · 2018Article
- Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers.Structure (London, England : 1993) · 2017Article
- The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.Journal of chemical theory and computation · 2017Article
- Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.Biochemistry · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Peptoids are a family of synthetic oligomers composed of N-substituted glycine units. Along with other "foldamer" systems, peptoid oligomer sequences can be predictably designed to form a variety of stable secondary structures. It is not yet evident if foldamer design can be extended to reliably create tertiary structure features that mimic more complex biomolecular folds and functions. Computational modeling and prediction of peptoid conformations will likely play a critical role in enabling complex biomimetic designs. We introduce a computational approach to provide accurate conformational and energetic parameters for peptoid side chains needed for successful modeling and design. We find that peptoids can be described by a "rotamer" treatment, similar to that established for proteins, in which the peptoid side chains display rotational isomerism to populate discrete regions of the conformational landscape. Because of the insufficient number of solved peptoid structures, we have calculated the relative energies of side-chain conformational states to provide a backbone-dependent (BBD) rotamer library for a set of 54 different peptoid side chains. We evaluated two rotamer library development methods that employ quantum mechanics (QM) and/or molecular mechanics (MM) energy calculations to identify side-chain rotamers. We show by comparison to experimental peptoid structures that both methods provide an accurate prediction of peptoid side chain placements in folded peptoid oligomers and at protein interfaces. We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design package previously validated in the context of protein design and structure prediction.
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.