[Chimera-users] Amino acid scanning

Aldo Segura aldosegura at gmail.com
Tue Jul 30 05:47:45 PDT 2013


Also, you should try with the FoldX program (http://foldx.crg.es/). The
program will take your  "wild type"structure and make the mutation
(whatever you want), then perform the calculation of the free energy. It is
worth nothing that the study of the metal ion-protein interaction by
molecular modeling, MD or related methods is not trivial.

Best regards,


2013/7/30 Alper Yilmaz <alperyilmaz at gmail.com>

> Hi,
> 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
> structure.
> 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.
> Thanks,
> 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
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

Aldo Segura-Cabrera
Postdoctoral Fellow
Division of Experimental Hematology and Cancer Biology
Cincinnati Children's Hospital Medical Center
3333 Burnet Ave, MLC 7019, Cincinnati OH 45229
e-mail: Aldo.Segura-Cabrera at cchmc.org <asegurac at ipn.mx>;
aldosegura at gmail.com
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