ArticleJournal of chemical information and modeling2020
Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.Briefings in bioinformatics · 2025Article
- Article
- Amino-Acid Characteristics in Protein Native State Structures.Biomolecules · 2024Article
- A feature engineering-based machine learning technique to detect and classify lung and colon cancer from histopathological images.Medical & biological engineering & computing · 2024Article
- Invariant point message passing for protein side chain packing.bioRxiv : the preprint server for biology · 2023Article
- Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs.Journal of chemical information and modeling · 2023Article
- Decoding CRISPR-Cas PAM recognition with UniDesign.Briefings in bioinformatics · 2023Article
- GeoPacker: A novel deep learning framework for protein side-chain modeling.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
- Identifying the Zoonotic Origin of SARS-CoV-2 by Modeling the Binding Affinity between the Spike Receptor-Binding Domain and Host ACE2.Journal of proteome research · 2020Article
- Identifying zoonotic origin of SARS-CoV-2 by modeling the binding affinity between Spike receptor-binding domain and host ACE2.bioRxiv : the preprint server for biology · 2020Article
- FASPR: an open-source tool for fast and accurate protein side-chain packing.Bioinformatics (Oxford, England) · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Protein rotamers refer to the conformational isomers taken by the side-chains of amino acids to accommodate specific structural folding environments. Since accurate modeling of atomic interactions is difficult, rotamer information collected from experimentally solved protein structures is often used to guide side-chain packing in protein folding and sequence design studies. Many rotamer libraries have been built in the literature but there is little quantitative guidance on which libraries should be chosen for different structural modeling studies. Here, we performed a comparative study of six widely used rotamer libraries and systematically examined their suitability for protein folding and sequence design in four aspects: (1) side-chain match accuracy, (2) side-chain conformation prediction, (3)
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