This is a test version of Biostars. For the public version, visit https://www.biostars.org.
To create amino acid substitution in protein structure

i have 3-D structure of protein (PDB format), and in that structure i want to create an amino acid substitution at specific position of protein and after that i need to know the global minimum energy of mutated structure.

Please suggest any software regarding above problem or any method i can follow

thank you

protein software
• 1,925 views • link
updated by fileyfood • fileyfood • written by shwetamgr1 • shwetamgr1

2 answers

Changing a single amino-acid is not that difficult (for example, see Swiss-Model or Modeller), but what you want appears to be more rigorous. I suggest FoldX or Rosetta, but beware that both of them have steep learning curves. FoldX has an explanation here and for Rosetta there are several, but you can probably start here.

• 0 views • link
written by Mensur Dlakic Mensur Dlakic

For more intensive analysis, you can consider MD simulations of the mutant protein where you relax the structure after mutation using tools like GROMACs or VMD

• 0 views • link
written by fileyfood • fileyfood

Log in to answer this question.

More posts like this