centerSelect

Selects a box-shaped isosurface around the active center.

The active center is approximated as a single point obtained as the geometric center of all the atoms from the active center.

1. Finding the position of the active center

In the context of this implementation a motife is a vector consisting of multiple aminoacids e.g. CYS GLY ALA. A set of motives is specified by the user. Then the pqr-file is scanned for any potential motifes. A list of found motives is returned. When multiple motifes are found the first occurence is taken. Then the atom-coordinates from the found motive are extracted. The geometrical center is then calculated. This geometric center is used as the approximation for the active center.

2. Iso-surface in close proximity to the active center

Given a single point (p.x,p.y,p.z) in 3D representing the active center a subset of the iso-surface is calculated as follows: Given a parameter boxSize and depth a square centered in p with height boxSize/2 and width boxSize/2 can be obtained. Then extruding this square along the z-axis from the front-side of the box to a position at p.z -depth one obtains a cuboid. Then all points from the iso-surface that lie within this box are used for further investigation.

For our paper we used as parameters boxSize = 30 and depth = 15 angstrom.

Call:

./centerSelect.sh _parametersFile_

where parametersFile specifies the file with the parameters. If you call

./centerSelect.sh

without any parameter a file with the name "parameters.txt" in the same folder is read in.

ParametersFile

The parametersFile contains the following parameters:

Parameter	Value	Description
path2centerSelect	/home/willy/RedoxChallenges/centerSelect/	path to this repo on the local machine
path2files	/home/willy/RedoxChallenges/centerSelect/Redox_old/Output/	path to the Output-folder where all folders with the proteins are stored
boxSize	30	size of the square that is to be drawn around the active centre parallel to the X- and Y-axis
depth	10	the box is drawn along the Z-axis.
eps	0.3	How much difference to the actual values -1.0 and 1.0 is tolerated.
onlyDoMissing	true	only select the active centres for the folders that do not already contain a file "activeCenter.csv".
SELECTBOX	false	do you want to select a subset of points that are in the box? the pts-file will then contain these points.

Folder Structure

└─── Redox_old
│   │   file011.txt
│   │   file012.txt
│   │
│   └─── Input
│       │   └───  pdb
│       │         │   001.pdb
│       │         │   002.pdb
│       │         │   ...
│       │   └───  pqr
│       │         │   001.pqr
│       │         │   002.pqr
│       │         │   ...
│   └─── Output
│       │   └───  001
│       │         │   001.pqr
│       │         │   001_el.tga
│       │         │   001_es.tga
│       │         │   001_ss.tga
│       │         │   001_neg.pts
│       │         │   001_pos.pts
│       │         │   001_pot.dx
│       │         │   apbs.in
│       │         │   ...
│       │   └───  002
│       │         │   002.pqr
│       │         │   002_el.tga
│       │         │   ...

In each folder in Output centerSelecter.R creates a file active_center.csv that specifies the number of atoms that are within the active centre. The files 001_neg.pts and 001_pos.pts contain the points of the iso-surface around the active centre that can be used in the next step to compare the similarity of the iso-surfaces.

AA_utility

Active Center Motifes

The file AA_utility/motifs3letterCode.txt contains the motifes of the active centers that the script will look for in the pdb-files.

CYS	ALA	HIS
CYS	GLY	ALA
CYS	ASN	HIS
...	...	...

AAs.csv

AAs.csv specifies the atom-chains that make up the aminoacids.

ALA	ARG	...
N	N	...
CA	CA	...
C	C	...
O	O	...
CB	CB	...
...	...	...

AA_lengths.csv

AA_lengths.csv specifies the lenghts of the atom-chains of the amino-acids.

ALA	ARG	ASN	ASP	...
10	24	14	14	...

Missing motifes

The file missing.txt contains the names of the proteins for which the script did not find an acitve center.

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