NMR resonance peak assignment is one of the key steps in solving an NMR protein structure. The assignment process links resonance peaks to individual residues of the target protein sequence, providing the prerequisite for establishing intra- and inter-residue spatial relationships between atoms. The assignment process is tedious and time-consuming, which could take many weeks. Though there exist a number of computer programs to assist the assignment process, many NMR labs are still doing the assignments manually to ensure quality. This paper presents (1) a new scoring system for mapping spin systems to residues, (2) an automated adjacency information extraction procedure from NMR spectra, and (3) a very fast assignment algorithm based on our previous proposed greedy filtering method and a maximum matching algorithm to automate the assignment process. The computational tests on 70 instances of (pseudo) experimental NMR data of 14 proteins demonstrate that the new score scheme has much better discerning power with the aid of adjacency information between spin systems simulated across various NMR spectra. Typically, with automated extraction of adjacency information, our method achieves nearly complete assignments for most of the proteins. The experiment shows very promising perspective that the fast automated assignment algorithm together with the new score scheme and automated adjacency extraction may be ready for practical use.
[NMR paper] Automated analysis of protein NMR assignments and structures.
Automated analysis of protein NMR assignments and structures.
Related Articles Automated analysis of protein NMR assignments and structures.
Chem Rev. 2004 Aug;104(8):3541-56
Authors: Baran MC, Huang YJ, Moseley HN, Montelione GT
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11-24-2010 10:01 PM
[NMR paper] Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignme
Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments.
Related Articles Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignments.
J Biomol NMR. 2003 Dec;27(4):313-21
Authors: Slupsky CM, Boyko RF, Booth VK, Sykes BD
Complete and accurate NMR spectral assignment is a prerequisite for high-throughput automated structure determination of biological macromolecules. However, completely automated assignment procedures generally encounter difficulties for all but the most ideal data...
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11-24-2010 09:16 PM
[NMR paper] A tracked approach for automated NMR assignments in proteins (TATAPRO).
A tracked approach for automated NMR assignments in proteins (TATAPRO).
Related Articles A tracked approach for automated NMR assignments in proteins (TATAPRO).
J Biomol NMR. 2000 Jun;17(2):125-36
Authors: Atreya HS, Sahu SC, Chary KV, Govil G
A novel automated approach for the sequence specific NMR assignments of 1HN, 13Calpha, 13Cbeta, 13C'/1Halpha and 15N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak...
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11-18-2010 09:15 PM
[NMR paper] Automated analysis of NMR assignments and structures for proteins.
Automated analysis of NMR assignments and structures for proteins.
Related Articles Automated analysis of NMR assignments and structures for proteins.
Curr Opin Struct Biol. 1999 Oct;9(5):635-42
Authors: Moseley HN, Montelione GT
Recent developments in protein NMR technology have provided spectral data that are highly amenable to analysis by advanced computer software systems. Specific data collection strategies, coupled with these computer programs, allow automated analysis of extensive backbone and sidechain resonance assignments and...
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11-18-2010 08:31 PM
Automated protein resonance assignments of magic angle spinning solid-state NMR spect
Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of β1 immunoglobulin binding domain of protein G (GB1)
Abstract Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for proteins not amenable to other methods. However, few automated analysis tools are currently available for MAS SSNMR. We present a methodology for automating protein resonance assignments of MAS SSNMR spectral data and its application to experimental peak lists of the...
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10-15-2010 05:16 PM
Automated protein resonance assignments of magic angle spinning solid-state NMR spect
Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of ?1 immunoglobulin binding domain of protein G (GB1).
Related Articles Automated protein resonance assignments of magic angle spinning solid-state NMR spectra of ?1 immunoglobulin binding domain of protein G (GB1).
J Biomol NMR. 2010 Oct 8;
Authors: Moseley HN, Sperling LJ, Rienstra CM
Magic-angle spinning solid-state NMR (MAS SSNMR) represents a fast developing experimental technique with great potential to provide structural and dynamics information for...
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10-12-2010 02:52 PM
[NMR paper] Automated analysis of protein NMR assignments using methods from artificial intellige
Automated analysis of protein NMR assignments using methods from artificial intelligence.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated analysis of protein NMR assignments using methods from artificial intelligence.
J Mol Biol. 1997 Jun 20;269(4):592-610
Authors: Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT
An expert system for determining resonance assignments from NMR spectra of proteins is...
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08-22-2010 03:31 PM
[NMR paper] Automated analysis of protein NMR assignments using methods from artificial intellige
Automated analysis of protein NMR assignments using methods from artificial intelligence.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Automated analysis of protein NMR assignments using methods from artificial intelligence.
J Mol Biol. 1997 Jun 20;269(4):592-610
Authors: Zimmerman DE, Kulikowski CA, Huang Y, Feng W, Tashiro M, Shimotakahara S, Chien C, Powers R, Montelione GT
An expert system for determining resonance assignments from NMR spectra of proteins is...