Amino-Acid Type and Secondary-Structure
Assignment by PLUQ
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. Please
cite the following paper when using PLUQ:
Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong, M.
J. Biomol. NMR. 56, 155-167 (2013).
The PACSY database scheme is described by
Lee et al
1. All chemical shifts are from the BioMagResBank (BMRB)
If you find bugs or have any questions
please contact: Keith
Download (from Dropbox):
sqlite3 database and PLUQ Python code (~60MB)
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.
2) Automated Sequential
Resonance Assignment by NSGA-II
and combination NSGA-II/MC programs are designed to predict the
assignment of protein solid-state NMR (SSNMR) spectra with
partial resonance overlap and missing peaks due to broad
linewidths, molecular motion, and low sensitivity. Please cite
the following paper when using these programs:
Y.; Fritzsching, K. J.; Hong, M. J. Biomol. NMR. 57, 281-296 (2013).
Monte-Carlo algorithm was previously published by Tycko and
coworkers 3, 4.
find bugs or have any questions please contact:
folder includes the input files of 6 test proteins.
"control_nsga.txt" is the control file used for NSGA2_assign
(modified NSGA-II program).
"control_gamc.txt" is the control file used for nsga2mc_assign
(Combo NSGA-II/MC program).
Fortran_programs: NSGA-II and NSGA2:MC.
MATLAB_program: This code allows you to analyze and display
the assignment output of the Fortran programs.
executable files: nsga2_assign and nsga2mc_assign
can be run directly in a Unix system.
you can download the Fortran source codes: main_program.f95
(main program), sub_source.f95 (contains all the
subroutines of the NSGA-II algorithm) and qsort.f95 (this
quicksort code is downloaded from the internet). All three files
should be added to a Fortran project and compiled to make an
executable file. A Fortran compiler is needed to do this.
must have MATLAB installed on your computer to use the Matlab
code postproc_assign.m. This code does not need to be
installed, simply navigate to the directory.
Lee, W.; Yu, W.; Kim, S.; Chang, I.; Lee, W.; Markley, J. L.
J. Biomol. NMR. 54, 169-179 (2012).
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
Res. 36, D402-8 (2008).
Tycko, R. and Hu, K. N. J. Magn. Reson. 205, 304-314
(4) Hu, K. N.; Qiang, W.; Tycko, R.
J. Biomol. NMR. 50, 267-276 (2011).