Question: How To Identify Cis And Trans Conformation Of Proline?
1
gravatar for aleeha
5.0 years ago by
aleeha10
aleeha10 wrote:

How can I find a proline is in cis and trans conformations? Is it possible to find from pdb files? or any tools available to find it?

protein • 3.2k views
ADD COMMENTlink modified 2.9 years ago by Hassan Rasouli10 • written 5.0 years ago by aleeha10
2
gravatar for wdiwdi
5.0 years ago by
wdiwdi380
Germany
wdiwdi380 wrote:

If you do not have a turnkey application for this problem, it is a typical application for a Cheminformatics Scripting Toolkit, such as our Cactvs software (see www.xemistry.com/academic for free academic packages)..

The approach is simple: Read the file, match a proline substructure, and compute the torsion angle of the relevant matched atoms: Here is a sample solution with the default Tcl interface language of the toolkit:

(The test PDB file with cis and trans proline fragments is from here)

set st [molfile read PRO-CONF.PDB]
# create proline substructure with C(=O)C stub.
# substructure atoms 1,2,4 and 5 are the atoms defining the torsion (atom 3 is the amide O)
set ss [ens create CC(=O)N1C(C=O)CCC1 smarts]  
# match the substructure and capture the atom mappings
match ss -mode all $ss $st amap          
# loop over all matches and compute the torsion angles
foreach match $amap {
    lassign [unzip $match 1] a1 a2 a3 a4 a5
    set torsion [atom torsion $st $a1 $a2 $a4 $a5]
    if {range($torsion,-10,10)} {
        puts "link $a1 $a2 $a4 $a5 is cis"
    } else {
        puts "link $a1 $a2 $a4 $a5 is trans"
    }
}

And in the current releases of the toolkit you can now also use Python as an alternative interface language, thanks to sponsorship by Vertex Inc:

st=Molfile.Read('PRO-CONF.PDB') 
ss=Ens('CC(=O)N1C(C=O)CCC1','smarts')
match('ss',ss,st,mode='all',atommapvariable='amap')
for match in amap:
    statoms=unzip(match,1)
    torsion=statoms[0].torsion(statoms[1],statoms[3],statoms[4])
    if torsion>=-10 and torsion<=10:
        print("link",statoms[0],statoms[1],statoms[3],statoms[4],"is cis")
    else:
        print("link",statoms[0],statoms[1],statoms[3],statoms[4],"is trans")
ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by wdiwdi380
0
gravatar for anna.chailyan
3.6 years ago by
anna.chailyan0 wrote:

Hey guys,

i just installed and started to play around with cactvs toolkit. Thanks a lot for the idea!!!! I used the above script to get the cis/trans state for proline. I would like to know if it is possible to run it for each chain in the pdb and also to write the residue number rather than the atom number.

 

Thanks!

ADD COMMENTlink written 3.6 years ago by anna.chailyan0
0
gravatar for Hassan Rasouli
2.9 years ago by
Kermanshah University of Medical science
Hassan Rasouli10 wrote:

thank you for your mentions. I installed Cactvs software. really it is a good software for finding any cis or trans conformation.

Thanks!

ADD COMMENTlink written 2.9 years ago by Hassan Rasouli10
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