I have an entire protein (the 5TH1B receptor crystallized with ergotamine) codenamed 4IAR on the RCSB. I need to create the flexibule residue file for the protein on AutoDock
Since there are many hundreds of amino acids that the protein receptor is made up of, it would be a laborious task to calculate or figure out the number of flexible residues on it and their points of torsion. Is there any way I can figure this out (perhaps via the RCSB page for 4IAR) or calculate it using AutoDock tools or another software even?
Best regards
I have basically gotten to the point of Exercise three B (page 19) of this manual:
http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf
Flexible Residues ➞ Choose Torsions in Currently Selected Residues…
but i simply don't know which residue of my receptor protein have felixble points. Any way I can figure this out or this the molecule simply too big, e.g. i need a software to calculate this for me?
I can see four possibilities (though there might be more):
A) Get multiple conformations (if there are any) from X-ray crystal structures of your protein...
B) Replace each amino acid residue in the protein (or the site of your interest) with all conformers from the rotamer library (see the attached link) or in PyMOL -> filter out those that would clash with some atoms nearby...
C) Generate an ensemble of structures using molecular dynamics simulation -> make lists of conformers of each amino acid residue...
D) Perform docking into rigid structures (representative snapshots from molecular dynamics simulation); this would be my first choice (if "A" is not an option).
http://www.dynameomics.org/rotamer/indexRotamer.aspx
- Badges
- Science topic
- Similar topics
- Chemistry
- Pharmacology
- Medical Pharmacology
- Clinical Pharmacology