ArticleJournal of biomolecular NMR2014
CSI 2.0: a significantly improved version of the Chemical Shift Index.
Article in Journal of biomolecular NMR, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- Backbone chemical shift and secondary structure assignments for mouse siderocalin.Biomolecular NMR assignments · 2024Article
- Structures, Interactions and Activity of the N-Terminal Truncated Variants of Antimicrobial Peptide Thanatin.Antibiotics (Basel, Switzerland) · 2024Article
- Recognition and coacervation of G-quadruplexes by a multifunctional disordered region in RECQ4 helicase.Nature communications · 2023Article
- The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs.RSC advances · 2023Review
- Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle.Frontiers in molecular biosciences · 2023Article
- NMR resonance assignments of the DNA binding domain of mouse Junctophilin-2.Biomolecular NMR assignments · 2022Article
- Human and Bacterial Toll-Interleukin Receptor Domains Exhibit Distinct Dynamic Features and Functions.Molecules (Basel, Switzerland) · 2022Article
- CSI-LSTM: a web server to predict protein secondary structure using bidirectional long short term memory and NMR chemical shifts.Journal of biomolecular NMR · 2021Article
- The Inherent Dynamics and Interaction Sites of the SARS-CoV-2 Nucleocapsid N-Terminal Region.Journal of molecular biology · 2021Article
- Structural and dynamical insights into the PH domain of p62 in human TFIIH.Nucleic acids research · 2021Article
- Merging NMR Data and Computation Facilitates Data-Centered Research.Frontiers in molecular biosciences · 2021Review
- Hairpin RNA-induced conformational change of a eukaryotic-specific lysyl-tRNA synthetase extension and role of adjacent anticodon-binding domain.The Journal of biological chemistry · 2020Article
- Local unfolding of the HSP27 monomer regulates chaperone activity.Nature communications · 2019Article
- FBP21's C-Terminal Domain Remains Dynamic When Wrapped around the c-Sec63 Unit of Brr2 Helicase.Biophysical journal · 2019Article
- Biliverdin Reductase B Dynamics Are Coupled to Coenzyme Binding.Journal of molecular biology · 2018Article
- The lineage-specific, intrinsically disordered N-terminal extension of monothiol glutaredoxin 1 from trypanosomes contains a regulatory region.Scientific reports · 2018Article
- The solution structure of monomeric CCL5 in complex with a doubly sulfated N-terminal segment of CCR5.The FEBS journal · 2018Article
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Abstract
Protein chemical shifts have long been used by NMR spectroscopists to assist with secondary structure assignment and to provide useful distance and torsion angle constraint data for structure determination. One of the most widely used methods for secondary structure identification is called the Chemical Shift Index (CSI). The CSI method uses a simple digital chemical shift filter to locate secondary structures along the protein chain using backbone (13)C and (1)H chemical shifts. While the CSI method is simple to use and easy to implement, it is only about 75-80% accurate. Here we describe a significantly improved version of the CSI (2.0) that uses machine-learning techniques to combine all six backbone chemical shifts ((13)Cα, (13)Cβ, (13)C, (15)N, (1)HN, (1)Hα) with sequence-derived features to perform far more accurate secondary structure identification. Our tests indicate that CSI 2.0 achieved an average identification accuracy (Q3) of 90.56% for a training set of 181 proteins in a repeated tenfold cross-validation and 89.35% for a test set of 59 proteins. This represents a significant improvement over other state-of-the-art chemical shift-based methods. In particular, the level of performance of CSI 2.0 is equal to that of standard methods, such as DSSP and STRIDE, used to identify secondary structures via 3D coordinate data. This suggests that CSI 2.0 could be used both in providing accurate NMR constraint data in the early stages of protein structure determination as well as in defining secondary structure locations in the final protein model(s). A CSI 2.0 web server (http://csi.wishartlab.com) is available for submitting the input queries for secondary structure identification.
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