CAMRA: Chemical shift based computer aided protein NMR assignments

Wolfram Gronwald, Leigh Willard, Timothy Jellard, Robert F. Boyko, Krishna Rajarathnam, David S. Wishart, Frank D. Sönnichsen, Brian D. Sykes

Research output: Contribution to journalArticle

48 Citations (Scopus)

Abstract

A suite of programs called CAMRA (Computer Aided Magnetic Resonance Assignment) has been developed for computer assisted residue-specific assignments of proteins. CAMRA consists of three units: ORB, CAPTURE and PROCESS. ORB predicts NMR chemical shifts for unassigned proteins using a chemical shift database of previously assigned homologous proteins supplemented by a statistically derived chemical shift database in which the shifts are categorized according to their residue, atom and secondary structure type. CAPTURE generates a list of valid peaks from NMR spectra by filtering out noise peaks and other artifacts and then separating the derived peak list into distinct spin systems. PROCESS combines the chemical shift predictions from ORB with the spin systems identified by CAPTURE to obtain residue specific assignments. PROCESS ranks the top choices for an assignment along with scores and confidence values. In contrast to other auto-assignment programs, CAMRA does not use any connectivity information but instead is based solely on matching predicted shifts with observed spin systems. As such, CAMRA represents a new and unique approach for the assignment of protein NMR spectra. CAMRA will be particularly useful in conjunction with other assignment methods and under special circumstances, such as the assignment of flexible regions in proteins where sufficient NOE information is generally not available. CAMRA was tested on two medium-sized proteins belonging to the chemokine family. It was found to be effective in predicting the assignment providing a database of previously assigned proteins with at least 30% sequence identity is available. CAMRA is versatile and can be used to include and evaluate heteronuclear and three-dimensional experiments.

Original languageEnglish (US)
Pages (from-to)395-405
Number of pages11
JournalJournal of Biomolecular NMR
Volume12
Issue number3
StatePublished - 1998
Externally publishedYes

Fingerprint

Chemical shift
Magnetic resonance
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Chemical Databases
Proteins
Computer program listings
Software
Chemokines
Artifacts
Noise
Databases
Atoms

Keywords

  • Assignment homology programs
  • Automatic

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Spectroscopy

Cite this

Gronwald, W., Willard, L., Jellard, T., Boyko, R. F., Rajarathnam, K., Wishart, D. S., ... Sykes, B. D. (1998). CAMRA: Chemical shift based computer aided protein NMR assignments. Journal of Biomolecular NMR, 12(3), 395-405.

CAMRA : Chemical shift based computer aided protein NMR assignments. / Gronwald, Wolfram; Willard, Leigh; Jellard, Timothy; Boyko, Robert F.; Rajarathnam, Krishna; Wishart, David S.; Sönnichsen, Frank D.; Sykes, Brian D.

In: Journal of Biomolecular NMR, Vol. 12, No. 3, 1998, p. 395-405.

Research output: Contribution to journalArticle

Gronwald, W, Willard, L, Jellard, T, Boyko, RF, Rajarathnam, K, Wishart, DS, Sönnichsen, FD & Sykes, BD 1998, 'CAMRA: Chemical shift based computer aided protein NMR assignments', Journal of Biomolecular NMR, vol. 12, no. 3, pp. 395-405.
Gronwald W, Willard L, Jellard T, Boyko RF, Rajarathnam K, Wishart DS et al. CAMRA: Chemical shift based computer aided protein NMR assignments. Journal of Biomolecular NMR. 1998;12(3):395-405.
Gronwald, Wolfram ; Willard, Leigh ; Jellard, Timothy ; Boyko, Robert F. ; Rajarathnam, Krishna ; Wishart, David S. ; Sönnichsen, Frank D. ; Sykes, Brian D. / CAMRA : Chemical shift based computer aided protein NMR assignments. In: Journal of Biomolecular NMR. 1998 ; Vol. 12, No. 3. pp. 395-405.
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