TY - JOUR
T1 - An integrated platform for automated analysis of protein NMR structures
AU - Huang, Yuanpeng Janet
AU - Moseley, Hunter N.B.
AU - Baran, Michael C.
AU - Arrowsmith, Cheryl
AU - Powers, Robert
AU - Tejero, Roberto
AU - Szyperski, Thomas
AU - Montelione, Gaetano T.
N1 - Funding Information:
We thank J. Aramini, A. Bhattacharya, G. Sahota, D. Snyder, G. V. T. Swapna, and D. Zheng for useful discussions and for their efforts over the past several years in developing automated NMR data analysis algorithms and software. The authors' recent work on automated NMR data analysis has been supported by the NIH Protein Structure Initiative (P50-GM62413).
PY - 2005
Y1 - 2005
N2 - Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress by the Northeast Structural Genomics Consortium in standardizing the NMR data collection process for protein structure determination and in building an integrated platform for automated protein NMR structure analysis. Our integrated platform includes the following principal steps: (1) standardized NMR data collection, (2) standardized data processing (including spectral referencing and Fourier transformation), (3) automated peak picking and peak list editing, (4) automated analysis of resonance assignments, (5) automated analysis of NOESY data together with 3D structure determination, and (6) methods for protein structure validation. In particular, the software AutoStructure for automated NOESY data analysis is described in this chapter, together with a discussion of practical considerations for its use in high-throughput structure production efforts. The critical area of data quality assessment has evolved significantly over the past few years and involves evaluation of both intermediate and final peak lists, resonance assignments, and structural information derived from the NMR data. Methods for quality control of each of the major automated analysis steps in our platform are also discussed. Despite significant remaining challenges, when good quality data are available, automated analysis of protein NMR assignments and structures with this platform is both fast and reliable.
AB - Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress by the Northeast Structural Genomics Consortium in standardizing the NMR data collection process for protein structure determination and in building an integrated platform for automated protein NMR structure analysis. Our integrated platform includes the following principal steps: (1) standardized NMR data collection, (2) standardized data processing (including spectral referencing and Fourier transformation), (3) automated peak picking and peak list editing, (4) automated analysis of resonance assignments, (5) automated analysis of NOESY data together with 3D structure determination, and (6) methods for protein structure validation. In particular, the software AutoStructure for automated NOESY data analysis is described in this chapter, together with a discussion of practical considerations for its use in high-throughput structure production efforts. The critical area of data quality assessment has evolved significantly over the past few years and involves evaluation of both intermediate and final peak lists, resonance assignments, and structural information derived from the NMR data. Methods for quality control of each of the major automated analysis steps in our platform are also discussed. Despite significant remaining challenges, when good quality data are available, automated analysis of protein NMR assignments and structures with this platform is both fast and reliable.
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U2 - 10.1016/S0076-6879(05)94005-6
DO - 10.1016/S0076-6879(05)94005-6
M3 - Article
C2 - 15808219
AN - SCOPUS:16244377434
SN - 0076-6879
VL - 394
SP - 111
EP - 141
JO - Methods in enzymology
JF - Methods in enzymology
ER -