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I want to introduce point mutations to a protein PDB file and automatically predict the 3D coordinates of a new amino acid residue in the mutated protein.

I used interactive Schrodinger's Maestro tool to mutate residues and minimize them to avoid clashes, however this time i want to automate the task and use some open source tools.

Is there any free software for this task?

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PDBFixer and pyMutate are simple, lightweight, free and open-source. Both don't do any optimizing, though, so you may have to run some molecular dynamics afterward to get what would be the right "orientation".

VMD would work for sure, I believe PyMOL too. They are both graphical interfaces but you can start them in text only mode (or just import pymol in a python script and use the Python API). They are free for particulars and academics, but given their renown you may already be using them.

If you're looking for something a tad more complete and that may adapt the side-chain to the surrounding environment I'd go with Modeller, which provides two example scripts to do point mutations (here and there).

If you don't want to just get the side-chain of this amino-acid right but actually strive to see some general backbone adaptation too then use PyRosetta. It can probably do what all the others do, too, but given it is 1 GB big it may be overkill. Any of the package coupled with molecular dynamics would also do the trick.

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  • $\begingroup$ Dear @O.Laprevote, thank you for your valuable answer! I actually tried running Rosetta's fixbb tool to mutate the truncated pdb residue with all missing atoms but one, however apparently it just ignores such residues, while mutating the truncated residues was my very task. $\endgroup$ – Nurlybek Amangeldiuly May 22 at 12:05
  • $\begingroup$ Modeller did the job very well for me. I am accepting this answer! $\endgroup$ – Nurlybek Amangeldiuly May 24 at 9:33

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