ArticleBioinformatics (Oxford, England)2011
Fast and accurate prediction of protein side-chain conformations.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Bioinformatic and computational biophysics tools for nanopore engineering: a review from standard approaches to machine learning advancements.Journal of nanobiotechnology · 2026Review
- To pack or not to pack: revisiting protein side-chain packing in the post-AlphaFold era.Briefings in bioinformatics · 2025Article
- Sifting through the noise: A survey of diffusion probabilistic models and their applications to biomolecules.Journal of molecular biology · 2025Review
- A curated rotamer library for common post-translational modifications of proteins.Bioinformatics (Oxford, England) · 2024Article
- Article
- H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing.ArXiv · 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
- OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling.Journal of chemical theory and computation · 2023Article
- Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity.Frontiers in molecular biosciences · 2023Article
- GeoPacker: A novel deep learning framework for protein side-chain modeling.Protein science : a publication of the Protein Society · 2022Article
- Evolution of the Automatic Rhodopsin Modeling (ARM) Protocol.Topics in current chemistry (Cham) · 2022Review
- OPUS-Rota4: a gradient-based protein side-chain modeling framework assisted by deep learning-based predictors.Briefings in bioinformatics · 2022Article
- Article
- InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps.Nucleic acids research · 2021Article
- Article
- Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.Journal of chemical information and modeling · 2020Article
- IDP-LZerD: Software for Modeling Disordered Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2020Article
- Computational reconstruction of atomistic protein structures from coarse-grained models.Computational and structural biotechnology journal · 2020Review
- Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics.PLoS computational biology · 2018Article
- Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking.Journal of computational chemistry · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryWe developed a fast and accurate side-chain modeling program [Optimized Side Chain Atomic eneRgy (OSCAR)-star] based on orientation-dependent energy functions and a rigid rotamer model. The average computing time was 18 s per protein for 218 test proteins with higher prediction accuracy (1.1% increase for χ(1) and 0.8% increase for χ(1+2)) than the best performing program developed by other groups. We show that the energy functions, which were calibrated to tolerate the discrete errors of rigid rotamers, are appropriate for protein loop selection, especially for decoys without extensive structural refinement. AVAILABILITY: OSCAR-star and the 218 test proteins are available for download at http://sysimm.ifrec.osaka-u.ac.jp/OSCAR CONTACT: standley@ifrec.osaka-u.ac.jp SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.