Non-sequential protein structure alignment algorithm
Project description
MICAN
Protein structure alignment program that can handle
- M: multiple-chain complexs
- I: inverse direction of SSEs
- C: Ca only models
- A: alternative alignments
- N: non-sequential alignments
Author information
Author: S. Minami, K. Sawada, and G. Chikenji
Web Site: http://www.tbp.cse.nagoya-u.ac.jp/MICAN
References
- BMC Bioinformatics 2013, 14(24), S. Minami, K. Sawada, and G. Chikenji
- Bioinformatics 2018, 34(19), S. Minami, K. Sawada, M Ota, and G. Chikenji
License
Easy instllation
pip install pymican
Python module usage
- install pymican
pip install pymican
- usage
# import module
from pymican import mican
# create object
m = mican()
# calculate alignment
aln = m.align(pdb1='pdbfile1', pdb2='pdbfile2', options='extra-mican-options')
# get TM-score, RMSD, etc.
print(aln.TMscore)
print(aln.rmsd)
Attributes of Alignment object
MICAN alignment class
Attributes
----------
outdict : dict
Alignment info
mode : str
Alignment mode
pdb1, pdb2 : str
PDB file path
size1, size2 : int
Size of protein structure
nalign : int
Number of aligned residues
rmsd : float
RMSD of aligned residues
TMscore : float
TM-score
sTMscore : float
SSE weighted TM-score
seq_identity : float
Sequence identity as percentage [0,100]
DALIscore : float
DALI z-score
SPscore : float
SP-score
TMscore1, TMscore2 : float
TM-score normalized by each protein length
coverage1, coverage2 : float
Aligned coverage for each protein length
translation_rot : numpy.array(3,3)
Rotation matrix for superposition protein1 on protein2
translation_vec : numpy.array(3)
Translation vector for superposition protein1 on protein2
alignment : pandas.DataFrame
Residue-Residue alignment info
alignlst : List[pandas.item]
Alignment info for iterator methods
Methods
-------
translate_xyz(xyz: np.array(N,3)) -> np.array(N,3)
Rotate & translate xyz coordinates
Compilation and usage
- To compile MICAN software: please type this command
% make
- To run MICAN software:
% mican protein1 protein2 -a align.aln -o sup.pdb
-- e.g. --
% mican test/test1.1.pdb test/test1.2.pdb -a align.aln -o sup.pdb
For more details, please read the usage.
USAGE: % mican protein1 protein2 [OPTION]
Description:
-f fast mode (same as "-g 15")
-s sequential (SQ) alignment mode
-w rewiring (RW) alignment mode
-r rewiring & reverse (RR) alignment mode
-R reverse constrained alignment mode
-x silent mode (without any output on the console)
-p print alignment progress
-c1 ChainIDs chain ID specifier for protein1 (e.g. -c1 A, -c1 ABC)
-c2 ChainIDs chain ID specifier for protein2
-o Filename superposition file (rasmol-script)
-a Filename alignment file
-m Filename translation matrix file
-n Integer number of solutions output (default=5)
-i Integer output i-th solution on stdout & superposition file
-t Integer selection score ([0]:sTMscore, 1:TMscore, 2:SPscore)
-g Integer number of GH candidates used (default=50)
-l Integer minimum segment length (default=3)
-d Real fix TM-score scaling factor d0
-q Real maximum distance between Ca atoms to be aligned (default=10.0)
Simple usage (SQ):
% mican protein1 protein2
% mican protein1 protein2 -a align.aln -o sup.pdb
Rewiring mode alignment (RW):
% mican protein1 protein2 -w
Rewiring & reverse mode alignment (RR):
% mican protein1 protein2 -r
To visualize superposition:
% mican protein1 protein2 -o sup.pdb
% rasmol -script sup.pdb
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