Related ArticlesSmartnotebook: 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 sets. Sources of these problems include difficulty in resolving correlations in crowded spectral regions, as well as complications arising from dynamics, such as weak or missing peaks, or atoms exhibiting more than one peak due to exchange phenomena. Smartnotebook is a semi-automated assignment software package designed to combine the best features of the automated and manual approaches. The software finds and displays potential connections between residues, while the spectroscopist makes decisions on which connection is correct, allowing rapid and robust assignment. In addition, smartnotebook helps the user fit chains of connected residues to the primary sequence of the protein by comparing the experimentally determined chemical shifts with expected shifts derived from a chemical shift database, while providing bookkeeping throughout the assignment procedure.
[NMR paper] A random graph approach to NMR sequential assignment.
A random graph approach to NMR sequential assignment.
Related Articles A random graph approach to NMR sequential assignment.
J Comput Biol. 2005 Jul-Aug;12(6):569-83
Authors: Bailey-Kellogg C, Chainraj S, Pandurangan G
Nuclear magnetic resonance (NMR) spectroscopy allows scientists to study protein structure, dynamics and interactions in solution. A necessary first step for such applications is determining the resonance assignment, mapping spectral data to atoms and residues in the primary sequence. Automated resonance assignment algorithms...
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[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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A multi-technique approach using LC-NMR, LC-MS, semi-preparative HPLC, HR-NMR and HR-
A multi-technique approach using LC-NMR, LC-MS, semi-preparative HPLC, HR-NMR and HR-MS for the isolation and characterization of low-level unknown impurities in GW876008, a novel corticotropin-release factor 1 antagonist.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles A multi-technique approach using LC-NMR, LC-MS, semi-preparative HPLC, HR-NMR and HR-MS for the isolation and characterization of low-level unknown impurities in GW876008, a novel corticotropin-release factor 1 antagonist.
J Pharm...
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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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[NMR paper] 1H NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignme
1H NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignments and identification of secondary structure elements.
Related Articles 1H NMR studies of the glucocorticoid receptor DNA-binding domain: sequential assignments and identification of secondary structure elements.
Biochemistry. 1990 Sep 25;29(38):9015-23
Authors: Härd T, Kellenbach E, Boelens R, Kaptein R, Dahlman K, Carlstedt-Duke J, Freedman LP, Maler BA, Hyde EI, Gustafsson JA
Two protein fragments containing the DNA-binding domain (DBD) of the...
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[NMR paper] A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: h
A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin.
Related Articles A novel approach for sequential assignment of 1H, 13C, and 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin.
Biochemistry. 1990 May 15;29(19):4659-67
Authors: Ikura M, Kay LE, Bax A
A novel approach is described for obtaining sequential assignment of the backbone 1H, 13C, and 15N...
Smartnotebook: a semi-automated approach to protein sequential NMR resonance assignme
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