Availability of experimental data enabled statistical inference of topological descriptors to its folding kinetics. Folding and unfolding rates have been correlated to short and long range contacts. Short contacts increases the propensity of local structural motifs like helix, beta hairpins, turns, whereas, long range interactions contributes the formation of beta structures and complex topologies. However, protein length has shown as positive correlation with logarithm of rate of folding, over the years many topological descriptors have been proposed to increase the predictability of protein folding/unfolding kinetics.
contact order parameters (relative and absolute) for pdbids for a defined Minimum residue distance to maximum residue distance cutoff
1.RCO: relative contact order,
2.ACO: absolute contact order,
3.SRO: short Range order,(2-4)
4.MRO: Medium Range Order,(5-8)
5.LRO: Long range Order,(>12)
6.TCD: Total Contact Distance, ()
7.N_alpha:
8.Effective Length (L,L^(1/2),L^(2/3),L^(3/5))
From contact matrix get indices(i,j) whose values are not zero. i-j is the sequence separion
between two contacting residues.
#Usage
---Analyzing multiple pdb files (input as list line terminated and tab separated)---
$ python contactOrders_List.py -h
usage: contactOrders_List.py [-h] [-p PDBFL] [-d PDBDIR] [-o OUTFL]
optional arguments:
-h, --help show this help message and exit
-p PDBFL pdb file and chain
-d PDBDIR PDB directory As in Only Beta:
./allPDbs/Data/PDB_files/
-o OUTFL output file name
----------- For individual pdb file--------------
python contactOrders.py -h
usage: contactOrders.py [-h] [-p PDBFL] [-c CHAIN]
optional arguments:
-h, --help show this help message and exit
-p PDBFL pdb file
-c CHAIN chain
#Reference
Multiple research article have been considered to analyze above topological descriptors, some are listed as folowing, Zou, Ozkon (2011, Proteins), Selveraja and Gorima (2004-2009 papers), Zhou and Zohu (2004), Ouyang and Liang (2002), Ivanakov and Baker (2003) +