Search PDB-format files for residue contacts
2
0
Entering edit mode
8 weeks ago
Suicyte ▴ 10

I am looking for a program that can process a large number of protein stuctures (PDB-format) and search the coordinates for a given criterion, or better, a combination of such criteria. A possible query would be: "return all instances where a lysine epsilon amino group makes a contact <3.5A) to a glutamate carboxy group", or something like that.

pdb structure coordinates • 211 views
ADD COMMENT
1
Entering edit mode
8 weeks ago
Mensur Dlakic ★ 14k

I don't know of a program that does exactly what you want, and would be surprised if it existed.

It would not be very difficult to write a python script to do this using BioPython. Once you read in all the atoms, it is simply a matter of going through all atoms that interest you and making a loop that calculates geometric distances between them.

distance = sqrt ( (x1-x2)^2 + (y1-y2)^2 + (z1-z2)^2 )

where x1, y1, z1 and x2, y2, z2 are the coordinates of the two atoms. I wrote a program a long time ago that does just that and outputs atoms and distances (see below), but it is written in Free Pascal and not suitable for sharing.

PS You probably want to exclude N+1 (and possibly N+2) residues, because many of them may have sidechains that are close but are not really interacting.

N MET 1 OD2 ASP 28 4.23 CA-CA 5.89 CB-CB 4.91 CA-CB 4.57 CB-CA 6.33
N MET 1 N PHE 266 4.36 CA-CA 5.25 CB-CB 4.97 CA-CB 5.19 CB-CA 5.45
N MET 1 C PHE 266 3.88 CA-CA 5.25 CB-CB 4.97 CA-CB 5.19 CB-CA 5.45
N MET 1 O PHE 266 2.71 CA-CA 5.25 CB-CB 4.97 CA-CB 5.19 CB-CA 5.45
CA MET 1 CG ASP 28 4.09 CA-CA 5.89 CB-CB 4.91 CA-CB 4.57 CB-CA 6.33
CA MET 1 OD2 ASP 28 3.34 CA-CA 5.89 CB-CB 4.91 CA-CB 4.57 CB-CA 6.33
CA MET 1 O PHE 266 3.84 CA-CA 5.25 CB-CB 4.97 CA-CB 5.19 CB-CA 5.45
ADD COMMENT
0
Entering edit mode
8 weeks ago
Jiyao Wang ▴ 170

You can use iCn3D Node.js script such as this one: https://github.com/ncbi/icn3d/blob/master/icn3dnode/ligand.js to batch process all structures. You need to modify the script a bit.

ADD COMMENT

Login before adding your answer.

Traffic: 2173 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6