ArticleJournal of biomolecular NMR2015
PPM_One: a static protein structure based chemical shift predictor.
Article in Journal of biomolecular NMR, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Targeting protein disorder: the next hurdle in drug discovery.Nature reviews. Drug discovery · 2025Review
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Structural Context Modulates the Conformational Ensemble of the Intrinsically Disordered Amino Terminus of α-Synuclein.Journal of the American Chemical Society · 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
- 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
- AssignSLP_GUI, a software tool exploiting AI for NMR resonance assignment of sparsely labeled proteins.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2022Article
- High-Resolution Conformational Analysis of RGDechi-Derived Peptides Based on a Combination of NMR Spectroscopy and MD Simulations.International journal of molecular sciences · 2022Article
- The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer.Autophagy · 2021Article
- DEEP picker is a deep neural network for accurate deconvolution of complex two-dimensional NMR spectra.Nature communications · 2021Article
- Informing NMR experiments with molecular dynamics simulations to characterize the dominant activated state of the KcsA ion channel.The Journal of chemical physics · 2021Article
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Using quantum chemistry to estimate chemical shifts in biomolecules.Biophysical chemistry · 2020Review
- Accelerating prediction of chemical shift of protein structures on GPUs: Using OpenACC.PLoS computational biology · 2020Article
- Accurate prediction of chemical shifts for aqueous protein structure on "Real World" data.Chemical science · 2020Article
- NMR Resonance Assignment Methodology: Characterizing Large Sparsely Labeled Glycoproteins.Journal of molecular biology · 2019Article
- Sixty-five years of the long march in protein secondary structure prediction: the final stretch?Briefings in bioinformatics · 2018Article
- Structural Characterization of a Heparan Sulfate Pentamer Interacting with LAR-Ig1-2.Biochemistry · 2018Article
- Measuring the signs of the methylJournal of biomolecular NMR · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM_One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.
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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.