I know we can do this using PyMol, PDBsum etc. But i want the details, atoms and hydrogen bonds involved in interaction of protein-ligand in text format.
Ultimately If i have to analyse 100s of docking result I can put that script in loop and get ready made 100 txt files with details of each docking.
I have already used summarize_results4.py from MGL Tool utilities.. it dint help
For tools,
pl see this link: http://www.imtech.res.in/bic/profunc.html
also see the postings on "List of drug discovery software perocesses"
"Has anyone compiled a list of software processes used in drug discovery... - on
"ResearchGate"
https://www.researchgate.net/.../Has_any_one_compiled_a_list_of_software_processes.
Apr 11, 2012 - Has any one compiled a list of software processes both open source and priced, used in ..... Ravi K. Sharma · Central Drug Research Institute
https://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwi-yLS6rsPPAhUIHGMKHY9TDpQQFggdMAA&url=https%3A%2F%2Fwww.researchgate.net%2Fpost%2FHas_any_one_compiled_a_list_of_software_processes_used_in_the_CADD&usg=AFQjCNH3WJFX3WjnaGZIyMyX-mzfjWFSCg
http://www.imtech.res.in/bic/profunc.html
https://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwi-yLS6rsPPAhUIHGMKHY9TDpQQFggdMAA&url=https%3A%2F%2Fwww.researchgate.net%2Fpost%2FHas_any_one_compiled_a_list_of_software_processes_used_in_the_CADD&usg=AFQjCNH3WJFX3WjnaGZIyMyX-mzfjWFSCg
It depends on what you mean by "interaction" . . . (Electrostatic interaction can act over long distances beyond the "first shell" of amino acid residues in the ligand-binding pocket). If you are interested in the "first shell" amino acid residues, you can calculate distances between the atoms (or groups of atoms) of the protein and the ligand, and apply a distance cut-off . . . to generate the "contact residues/atoms list". You might need to play with the representative coordinates of each residue (atoms/groups) and the ligand, and with the distance cut-off . . .
---
# For every atom in the protein...
for i in protein:
# Get the xyz coordinates...
xi...
yi...
zi...
# For every ligand (pose)...
for ligand in ligands:
# For every atom in the ligand...
for j in ligand:
# Get the xyz coordinates...
xj...
yj...
zj...
# Calculate distance between "i" and "j"...
d = ((xj - xi)**2 + (yj - yi)**2 + (zj -zi)**2)**0.5
# Apply cut-off...
if d
Interacting residues can be determined by various approaches, for examples, you can consider buried surface residues or simply can take a cutoff distance from the nearest atom of interacting subunit. For hydrogen bond, HBPlus can be used. Basic knowledge of python is enough to serve these purposes. You can try your luck at github also.
All the best..
@Sunandan Mukherjee @Prof. Ravi K. Sharma. Thank you all for the help
@Martin Klvana
Script idea provided by you will give the atoms in radius of given cut off, but there are more parameters to be defined like donors and acceptors and all other conditions required that defines hydrogen bond. But I appreciate the efforts for the same from you.
I was searching side by side and I came across this python script "Binana_1_2" , n open source python script written by NBCR. It gives all interactions like pi-pi , hydrogen bonds, salt-bridges and so on.
Obviously you will need numpy which is present in MGL Tool. Just have to add the PYTHONPATH to that folder.
I also wrote an adaptor script which automates the complete docking and gets docking details in text format explaining all interactions using "BINANA" script.
I hope this can help you in future if needed.
http://nbcr.ucsd.edu/data/sw/hosted/binana/
Rishikesh Sarode The link provided by you is not working. Please share a working link with us.
Hi.
This is a late reply, but in case someone is still looking for such a script - I've made one.
There are still some things to be implemented but, at this point, the script can analyze multiple pdb files and output the distances between amino acids and/or water molecules (or output True/False if desired).
https://github.com/Zemaxe/AALI
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