Best tool to compare sidechains effects

[leleonp]

Which should be the best tool to compare sidechains in an ensemble of proteins (same protein with different mutations)? nma.pdbs with ff=sdENM or aanma.pdbs?? Thanks in advance

Luis

[Xinqiu Yao]

Hi Luis,

This is a good question but unfortunately I have no answer yet. Both models have amino acid information included and probably can response to point mutations. However, without apparent conformational change, I doubt that these responses can be detected for either model. Why not give it a try for both and see which one is more suitable? Note that we have recently improved 'aanma()' to make it several times faster than before. Check out the latest feature_aanma branch, pay attention to the rtb or reduced option in aanma().