ArticleThe journal of physical chemistry. B2022
Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins.
Article in The journal of physical chemistry. B, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- A Bayesian Framework with Dirichlet Priors and Spatial Smoothing for Protein Rotamer Prediction.International journal of molecular sciences · 2026Article
- intDesc-AbMut: A Tool for Describing and Understanding How Antibody Mutations Impact Their Environmental Interactions.Computational and structural biotechnology journal · 2026Article
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
- Article
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2 authors.
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Abstract
Rotamers, namely amino acid side chain conformations common to many different peptides, can be compiled into libraries. These rotamer libraries are used in protein modeling, where the limited conformational space occupied by amino acid side chains is exploited. Here, we construct a sequence-dependent rotamer library from simulations of all possible tripeptides, which provides rotameric states dependent on adjacent amino acids. We observe significant sensitivity of rotamer populations to sequence and find that the library is successful in locating side chain conformations present in crystal structures. The library is designed for applications with basin-hopping global optimization, where we use it to propose moves in conformational space. The addition of rotamer moves significantly increases the efficiency of protein structure prediction within this framework, and we determine parameters to optimize efficiency.
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