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PLUQ
(PACSYLite Unified
Query) |
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Description:
This script/code queries a database to help predict possible amino acid residue types and secondary structure assignments from 13C and/or 15N chemical shifts. There is a paper that describes this code and related topics submitted to J. BioMol NMR 1. The PACSY database scheme is described by Lee et al 2. All chemical shifts are from the BioMagResBank (BMRB) 3. Structural classification were generated using STRIDE 4. If you find bugs or have any questions please contact: Keith Fritzsching (kfritzsc@iastate.edu) Download (from Dropbox): PACSYlite sqlite3 database and PLUQ Python code (~60MB) Install: You must have Python 2.7 on your computer or Python 2.x and the necessary packages (argparse, sqlite3...). If you have troubles install the latest version of Python. We recommend using the free Enthough Python distribution, which has a one click installer for common operating systems and includes many useful Python packages with a scientific focus. This code does not need to be installed, simply navigate to the directory. Examples:
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References:
(1)
Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr,K.; Hong, Mei.
2013, 'submitted' (2)
Lee, W.; Yu, W.; Kim, S.; Chang, I.; Lee, W.; Markley, J. L.
Journal of Biomolecular NMR 2012, 54, 169-179. (3)
Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F.; Harano, Y.;
Ioannidis, Y. E.; Lin, J.; Livny, M.; Mading, S.;
Maziuk, D.; Miller, Z.; Nakatani, E.; Schulte, C. F.; Tolmie, D.
E.; Kent Wenger, R.; Yao, H.; Markley, J. L. Nucleic Acids
Research 2008, 36, D402-8. (4) Heinig,
M.; Frishman, D. Nucleic Acids Research 2004, 32,
W500-2. |
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Please send comments or suggestions about the website to: tuowang@iastate.edu |
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