Hi Wenhe , You can mutate the desired residue in 'pymol' (save the new pdb structures) and run them for molecular dynamic simulations (in Gromacs, Desmond etc.) to see the stability of your protein [for the full length protein or its segments] (by checking RMSD and RMSF values). You can analyze various aspects using the trajectory files and ensemble average values. Hope this helps.
Best!! Debasish CSIR- Senior Research Fellow (PhD Scholar) Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html ----- Original Message ----- From: "WENHE ZHONG" <wenhezhong.xmu....@gmail.com> To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, November 24, 2017 10:38:28 PM Subject: [ccp4bb] Predict effects of mutations on protein stability and protein-protein interaction Dear Community, A little bit out-of-topic here. We have a few interesting sites would like to mutate on proteins to test the protein stability and improve the protein-protein interactions. Before moving forward to the site mutagenesis experiment, we like to do some prediction first to narrow down the candidates. We only know that SDM is good server to predict the protein stability. Do you have other servers or softwares can recommend? We can do a cross comparison. Thanks. Kind regards, Wenhe
