Hello everyone;
I've isolated a 12-mer peptide against PDL-1 from a phage library. During in silico analysis I realized that my peptide tends to bind other sites rather than desired binding site! I tried to do an Alanine scanning to check which substitution would change the binding mode, but it's a little complicated to decide what other amino acid substitution would be desired.
Can anyone suggest me any software or web server to do this job? I've heard about "OSPREY" but I need more options to choose :)
Thank you all
Dear Ramin Ekhteiari;
I want to do an in silico analysis through which I substitute some residues with others and check if binding mode is improved toward the desired binding site by means of docking tools. As long as this job is somehow complicated, I need some useful web servers or softwares to do it for me.
Thank you
if you want to control the parameters yourself I recommend software like: AMBER, NAMD or Rosseta
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