To be more precise in how can we dock the protein onto specific site of DNA? If possible also tell me how could we isolate the structure of DNA sequence (in PDB format).
Thank You Jorge Sir,
Can You help me out in the same? can you suggest me some softwares which you feel are authentic?
Dear Tarun,
I suggest Autodock 4 for DNA docking...
autodock.scripps.edu/
Hope it helps,
HHA
Hello Hamed Sir,
Can you specify me how can we use autodock 4 for DNA docking
Autodock4 use semi empirical scoring function simulates VdW, electrostatics, desolvation as well as ligands (protein in your case) torsional degrees of freedom. However, treating protein as flexible during docking is impractical as maximum rotable bonds allowed in Autodock is about 30 and convergence for this kind of search is difficult to converge.
if you insist on using autodock4, and your protein size is quite small with only one domain (i.e. no major protein rearrangement during DNA binding) you can do the reverse, dock DNA to the protein using flexible protein side chains and stiff all DNAs tortional bonds during docking so to be treated as single block.
HADDOCK (High Ambiguity Data Driven Docking) has protein-DNA and protein-RNA docking capabilities. Furthermore, you can use restraints (i.e. information on specific interaction sites) to direct the docking simulation to a specified part of the molecule. You can find more about it in their websites:
http://haddock.science.uu.nl/services/HADDOCK/haddock.php
http://www.nmr.chem.uu.nl/haddock/
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