ArticleProteins2009
X-ray vs. NMR structures as templates for computational protein design.
Article in Proteins, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Re-engineering of a carotenoid-binding protein based on NMR structure.Protein science : a publication of the Protein Society · 2024Article
- Lactobacillus for ribosome peptide editing cancer.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2023Review
- Article
- Core packing of well-defined X-ray and NMR structures is the same.Protein science : a publication of the Protein Society · 2022Article
- The accuracy of protein structures in solution determined by AlphaFold and NMR.Structure (London, England : 1993) · 2022Article
- Analyses of protein cores reveal fundamental differences between solution and crystal structures.Proteins · 2020Article
- EvoEF2: accurate and fast energy function for computational protein design.Bioinformatics (Oxford, England) · 2020Article
- Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries.Journal of chemical information and modeling · 2020Article
- Computational Analysis of Energy Landscapes Reveals Dynamic Features That Contribute to Binding of Inhibitors to CFTR-Associated Ligand.The journal of physical chemistry. B · 2019Article
- Recent advances in automated protein design and its future challenges.Expert opinion on drug discovery · 2018Review
- An overview of recent molecular dynamics applications as medicinal chemistry tools for the undruggable site challenge.MedChemComm · 2018Review
- Computer-aided design of amino acid-based therapeutics: a review.Drug design, development and therapy · 2018Review
- Rosetta:MSF: a modular framework for multi-state computational protein design.PLoS computational biology · 2017Article
- Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.Journal of molecular biology · 2016Article
- Optimization of rotamers prior to template minimization improves stability predictions made by computational protein design.Protein science : a publication of the Protein Society · 2015Article
- Algorithmic approaches to protein-protein interaction site prediction.Algorithms for molecular biology : AMB · 2015Article
- Article
- Modeling protein-peptide recognition based on classical quantitative structure-affinity relationship approach: implication for proteome-wide inference of peptide-mediated interactions.The protein journal · 2013Article
- Energy functions in de novo protein design: current challenges and future prospects.Annual review of biophysics · 2013Review
- The structure of neuronal calcium sensor-1 in solution revealed by molecular dynamics simulations.PloS one · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Certain protein-design calculations involve using an experimentally determined high-resolution structure as a template to identify new sequences that can adopt the same fold. This approach has led to the successful design of many novel, well-folded, native-like proteins. Although any atomic-resolution structure can serve as a template in such calculations, most successful designs have used high-resolution crystal structures. Because there are many proteins for which crystal structures are not available, it is of interest whether nuclear magnetic resonance (NMR) templates are also appropriate. We have analyzed differences between using X-ray and NMR templates in side-chain repacking and design calculations. We assembled a database of 29 proteins for which both a high-resolution X-ray structure and an ensemble of NMR structures are available. Using these pairs, we compared the rotamericity, chi(1)-angle recovery, and native-sequence recovery of X-ray and NMR templates. We carried out design using RosettaDesign on both types of templates, and compared the energies and packing qualities of the resulting structures. Overall, the X-ray structures were better templates for use with Rosetta. However, for approximately 20% of proteins, a member of the reported NMR ensemble gave rise to designs with similar properties. Re-evaluating RosettaDesign structures with other energy functions indicated much smaller differences between the two types of templates. Ultimately, experiments are required to confirm the utility of particular X-ray and NMR templates. But our data suggest that the lack of a high-resolution X-ray structure should not preclude attempts at computational design if an NMR ensemble is available.
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