How do I do side chain modeling for protein point mutations i.e. which software do I need to use?
I have downloaded and install scwrl but could not understand how to use it, and there are no tutorials online. If u know how to use kindly help me
Hey thank you very much for that ,and need lil more help, just tell me the format that i need to type for input, when i am giving input it is returning error msg. Thank you
Hi...
download Scwrl4 version and install your PC, then if you want to point mutation, delete side-chains atoms for particular aminoacid.
Mich that's great I understood that, but nw i am getting an error like can not open file seq, I have used fasta ormat itself I'm uploading that command prompt just see where i'm going wrong. i even tried the seq in fasta format also that is with > symbol still not working
Yeah may be, i ll try all other possible ways. Thanks a ton for helping me out.
Hi, Y cant we use Modeller for mutation?
mutate_selection.py script does the same, Mutate model does optimization of the side chain of the mutated residue which former one doesnt do it.
I understood that Scwrl4 doesnt disturb the backbone.
Could you state which one is better; modeller or Scwrl4?
Another alternative is FoldX from the L. Serrano group ULR http://foldxsuite.crg.eu . This is also able to handle incomplete chains quite well. I think, you may also are supposed to work on only one single protein chain. So if there were several chains in one PDB file, grep the the chains, save them in different files (e.g. _A.pdb , _B.pdb, ...) and work particularly on these. Kr, MM
after performing Scwrl4, how to validate the reliability of the output (predicted stucture)?
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