ArticleJournal of biomolecular NMR2012
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles.
Article in Journal of biomolecular NMR, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Complete NMR assignment for 275 of the most common dipeptides in intrinsically disordered proteins.Scientific data · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Toward a unified framework for determining conformational ensembles of disordered proteins.Nature methods · 2026Review
- Top-Down Scoring of Spectral Fitness by Image Analysis for Protein Structure Validation.Journal of chemical information and modeling · 2026Article
- NMR data processing, visualization, analysis and structure calculation with NMRFx.Communications chemistry · 2025Article
- Pantinin-Derived Peptides against Veterinary Herpesviruses: Activity and Structural Characterization.ChemMedChem · 2025Article
- Decoding phospho-regulation and flanking regions in autophagy-associated short linear motifs.Communications biology · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- UCBShift 2.0: Bridging the Gap from Backbone to Side Chain Protein Chemical Shift Prediction for Protein Structures.Journal of the American Chemical Society · 2024Article
- EFG-CS: Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models.Protein science : a publication of the Protein Society · 2024Article
- Resolution in cryogenic solid state NMR: Challenges and solutions.Protein science : a publication of the Protein Society · 2024Review
- Ensemble-based design of tau to inhibit aggregation while preserving biological activity.Research square · 2024Article
- Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2023Article
- High-Resolution Conformational Analysis of RGDechi-Derived Peptides Based on a Combination of NMR Spectroscopy and MD Simulations.International journal of molecular sciences · 2022Article
- Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins.PLoS computational biology · 2022Article
- Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel.The Journal of chemical physics · 2021Article
- Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs.Frontiers in molecular biosciences · 2021Article
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Analysis of conformational exchange processes using methyl-TROSY-based Hahn echo measurements of quadruple-quantum relaxation.Magnetic resonance (Gottingen, Germany) · 2021Article
- Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC.PLoS computational biology · 2020Article
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2 authors.
Funding
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Abstract
The combination of the wide availability of protein backbone and side-chain NMR chemical shifts with advances in understanding of their relationship to protein structure makes these parameters useful for the assessment of structural-dynamic protein models. A new chemical shift predictor (PPM) is introduced, which is solely based on physical-chemical contributions to the chemical shifts for both the protein backbone and methyl-bearing amino-acid side chains. To explicitly account for the effects of protein dynamics on chemical shifts, PPM was directly refined against 100 ns long molecular dynamics (MD) simulations of 35 proteins with known experimental NMR chemical shifts. It is found that the prediction of methyl-proton chemical shifts by PPM from MD ensembles is improved over other methods, while backbone Cα, Cβ, C', N, and H(N) chemical shifts are predicted at an accuracy comparable to the latest generation of chemical shift prediction programs. PPM is particularly suitable for the rapid evaluation of large protein conformational ensembles on their consistency with experimental NMR data and the possible improvement of protein force fields from chemical shifts.
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