I would like to change an aminoacid in a protein sequence. Can someone suggest me a software? Can I change the sequence directly in the pdb file? If yes, how?
To do simple mutation Pymol should do fine: http://www.pymolwiki.org/index.php/Mutagenesis
The standard and probably most-used software to get optimal rotamers of the mutated amino acid is scwrl4 (http://dunbrack.fccc.edu/scwrl4/) which is free for academic purposes.
Goddard at Caltech has an even better protocol for side-chain placement called SCREAM (www.wag.caltech.edu/publications/sup/pdf/776.pdf), unfortunately it's nor implemented in any free software.
Assessment of protein side-chain conformation prediction methods in different residue environments
http://onlinelibrary.wiley.com/doi/10.1002/prot.24552/full
http://fold.doe-mbi.ucla.edu/genemine/ by C Lee and S Subbiah from M Levitt group
I used Genemine some 15 years back. This is a trivial problem these days.
Protein sequence analysis software- Swiss PDB Viewer, GOR, Swiss Model and BioEdit.
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