[Chimera-users] Amino acid scanning

Alper Yilmaz alperyilmaz at gmail.com
Tue Jul 30 04:35:02 PDT 2013


We are conducting a study to figure out the best amino acid mutation for
increased affinity for a particular metal ion.
I'm pretty novice in this field so I wanted to get suggestions as to my
approach makes sense or not.
I'll write a demo script (more probably python script) to substitute
certain amino acids with all standard amino acids and then minimize the
As far as I know, Chimera can not calculate free energy, so I will save the
PDB files and then use another program to calculate the free energy.

My first question is, whether the commands below are appropriate for my
purpose or not? The sample below is a snippet from an exhaustive list. I
preferred to save the information regarding clashes before the minimization
just to keep record.

swapaa ala :22.a
findclash :22.a log true saveFile clash_report_22ala
minimize nogui true
write #0 test_22ala
swapaa val :22.a
findclash :22.a log true saveFile clash_report_22val
minimize nogui true
write #0 test_22val
swapaa ile :22.a
findclash :22.a log true saveFile clash_report_22ile
minimize nogui true
write #0 test_22ile

My second question is, when I have many PDB files, which software is
suitable for calculating the free energy for each.


Assist.Prof.Dr. Alper YILMAZ
Department of Bioengineering
Faculty of Chemical and Metallurgical Engineering
Yildiz Technical University
Esenler, Istanbul/TURKEY 34210
Phone: +90.212.383-4657 (office)
Fax: +90.212.383-4625
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