Related ArticlesA 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 lists from a set of triple resonance spectra which correlate 1HN and 15N chemical shifts with those of 13Calpha, 13Cbeta and 13C'/1Halpha. The information derived from such correlations is used to create a 'master-_list' consisting of all possible sets of 1HN(i), 15N(i)13Calpha(i),13Cbeta(i) 13C'beta(i)/1Halpha(i), 13Calpha(i-1), 13Cbeta(i-1) and 13C'(i-1)/1Halpha(i-1) chemical shifts. On the basis of an extensive statistical analysis of 13Calpha and 13Cbeta chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master_list and also to translate the protein primary sequence into an array called pps_array. The program then uses the master_list to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so. each assigned residue is tracked in an array called assig_array, with the two-digit code assigned earlier. The assig_array is then mapped onto the pps_array for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18-42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the master_list created for the test proteins.
[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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[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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[NMR paper] Automated protein NMR resonance assignments.
Automated protein NMR resonance assignments.
Related Articles Automated protein NMR resonance assignments.
Proc IEEE Comput Soc Bioinform Conf. 2003;2:197-208
Authors: Wan X, Xu D, Slupsky CM, Lin G
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,...
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[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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[NMR paper] An automated approach for defining core atoms and domains in an ensemble of NMR-deriv
An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures.
Related Articles An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures.
Protein Eng. 1997 Jun;10(6):737-41
Authors: Kelley LA, Gardner SP, Sutcliffe MJ
A single NMR-derived protein structure is usually deposited as an ensemble containing many structures, each consistent with the restraint set used. The number of NMR-derived structures deposited in the Protein Data Bank (PDB) is...
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[NMR paper] An automated approach for defining core atoms and domains in an ensemble of NMR-deriv
An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures.
Related Articles An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures.
Protein Eng. 1997 Jun;10(6):737-41
Authors: Kelley LA, Gardner SP, Sutcliffe MJ
A single NMR-derived protein structure is usually deposited as an ensemble containing many structures, each consistent with the restraint set used. The number of NMR-derived structures deposited in the Protein Data Bank (PDB) is...
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[NMR paper] An automated approach for clustering an ensemble of NMR-derived protein structures in
An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Related Articles An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies.
Protein Eng. 1996 Nov;9(11):1063-5
Authors: Kelley LA, Gardner SP, Sutcliffe MJ
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A probabilistic approach for validating protein NMR chemical shift assignments
Abstract It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program...
A tracked approach for automated NMR assignments in proteins (TATAPRO).
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