ArticleJournal of biomolecular NMR2003
Fully automated sequence-specific resonance assignments of hetero- nuclear protein spectra.
Article in Journal of biomolecular NMR, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 51 citations in OpenAlex.
- VirtualSpectrum, a tool for simulating peak list for multi-dimensional NMR spectra.Journal of biomolecular NMR · 2014Article
- Automated robust and accurate assignment of protein resonances for solid state NMR.Journal of biomolecular NMR · 2014Article
- Reliability of exclusively NOESY-based automated resonance assignment and structure determination of proteins.Journal of biomolecular NMR · 2013Article
- Automated solid-state NMR resonance assignment of protein microcrystals and amyloids.Journal of biomolecular NMR · 2013Article
- Exclusively NOESY-based automated NMR assignment and structure determination of proteins.Journal of biomolecular NMR · 2011Article
- Binding site identification and structure determination of protein-ligand complexes by NMR a semiautomated approach.Methods in enzymology · 2011Article
- Structure-oriented methods for protein NMR data analysis.Progress in nuclear magnetic resonance spectroscopy · 2010Review
- A practical implementation of cross-spectrum in protein backbone resonance assignment.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2010Article
- Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.Journal of biomolecular NMR · 2009Article
- Automated protein structure calculation from NMR data.Journal of biomolecular NMR · 2009Article
- Automated structure determination from NMR spectra.European biophysics journal : EBJ · 2009Review
- Automated amino acid side-chain NMR assignment of proteins using (13)C- and (15)N-resolved 3D [ (1)H, (1)H]-NOESY.Journal of biomolecular NMR · 2008Article
- Graphical interpretation of Boolean operators for protein NMR assignments.Journal of biomolecular NMR · 2008Article
- PASA--a program for automated protein NMR backbone signal assignment by pattern-filtering approach.Journal of biomolecular NMR · 2006Article
- Probabilistic Identification of Spin Systems and their Assignments including Coil-Helix Inference as Output (PISTACHIO).Journal of biomolecular NMR · 2005Article
- GANA--a genetic algorithm for NMR backbone resonance assignment.Nucleic acids research · 2005Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Full automation of the analysis of spectra is a prerequisite for high-throughput NMR studies in structural or functional genomics. Sequence-specific assignments often form the major bottleneck. Here, we present a procedure that yields nearly complete backbone and side chain resonance assignments starting from a set of heteronuclear three-dimensional spectra. Neither manual intervention, e.g., to correct lists obtained from peak picking before feeding these to an assignment program, nor protein-specific information, e.g., structures of homologous proteins, were required. By combining two earlier published procedures, AUTOPSY [Koradi et al. (1998) J. Magn. Reson., 135, 288-297] and GARANT [Bartels et al. (1996) J. Biomol. NMR, 7, 207-213], with a new program, PICS, all necessary steps from spectra analyses to sequence-specific assignments were performed fully automatically. Characteristic features of the present approach are a flexible design allowing as input almost any combination of NMR spectra, applicability to side chains, robustness with respect to parameter choices (such as noise levels) and reproducibility. In this study, automated resonance assignments were obtained for the 14 kD blue copper protein azurin from P. aeruginosa using five spectra: HNCACB, HNHA, HCCH-TOCSY, 15N-NOESY-HSQC and 13C-NOESY-HSQC. Peaks from these three-dimensional spectra were filtered and calibrated with the help of two two-dimensional spectra: 15N-HSQC and 13C-HSQC. The rate of incorrect assignments is less than 1.5% for backbone nuclei and about 3.5% when side chain protons are also considered.
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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.