ArticleJournal of the American Chemical Society2010
Development of a rotamer library for use in beta-peptide foldamer computational design.
Article in Journal of the American Chemical Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Library docking for Cannabinoid-2 Receptor ligands.bioRxiv : the preprint server for biology · 2026Article
- Metal Cation-Binding Mechanisms of Q-Proline Peptoid Macrocycles in Solution.Journal of chemical information and modeling · 2021Article
- Review
- Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers.Structure (London, England : 1993) · 2017Article
- Realistic sampling of amino acid geometries for a multipolar polarizable force field.Journal of computational chemistry · 2015Article
- Conformational properties of 1,4- and 1,5-substituted 1,2,3-triazole amino acids – building units for peptidic foldamers.Organic & biomolecular chemistry · 2015Article
- Comparative mechanistic studies of brilacidin, daptomycin, and the antimicrobial peptide LL16.Antimicrobial agents and chemotherapy · 2014Article
- A rotamer library to enable modeling and design of peptoid foldamers.Journal of the American Chemical Society · 2014Article
- Article
- Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).PloS one · 2013Article
- Relationship between side-chain branching and stoichiometry in β(3)-peptide bundles.Tetrahedron · 2012Article
- The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.Biophysical journal · 2012Article
- Antibacterial mechanism of action of arylamide foldamers.Antimicrobial agents and chemotherapy · 2011Article
- Computational design of a self-assembling β-peptide oligomer.Organic letters · 2010Article
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Authors and funding
4 authors.
Funding
Abstract
Foldamers present a particularly difficult challenge for accurate computational design compared to the case for conventional peptide and protein design due to the lack of a large body of structural data to allow parametrization of rotamer libraries and energies. We therefore explored the use of molecular mechanics for constructing rotamer libraries for non-natural foldamer backbones. We first evaluated the accuracy of molecular mechanics (MM) for the prediction of rotamer probability distributions in the crystal structures of proteins is explored. The van der Waals radius, dielectric constant and effective Boltzmann temperature were systematically varied to maximize agreement with experimental data. Boltzmann-weighted probabilities from these molecular mechanics energies compare well with database-derived probabilities for both an idealized alpha-helix (R = 0.95) as well as beta-strand conformations (R = 0.92). Based on these parameters, de novo rotamer probabilities for secondary structures of peptides built from beta-amino acids were determined. To limit computational complexity, it is useful to establish a residue-specific criterion for excluding rare, high-energy rotamers from the library. This is accomplished by including only those rotamers with probability greater than a given threshold (e.g., 10%) of the random value, defined as 1/n where n is the number of potential rotamers for each residue type.
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