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
Hi, 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, Aldo 2013/7/30 Alper Yilmaz <alperyilmaz@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
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-- ========================================= 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@cchmc.org <asegurac@ipn.mx>; aldosegura@gmail.com =========================================
Hi Alper, I don't have an answer for the second question -- there are many possibilities which I haven't used or compared with each other -- but you are right that Chimera does not calculate free energies. As for the first question, your commands look reasonable to me. For the clash-report and PDB files you might want to include the whole pathname (including file location). On my Mac it might be something like this: write #0 /Users/meng/Desktop/mutations/test_22ile.pdb Also if you were rotating the view of the structure around but you want to keep the same coordinates as the original structure (except for the mutation, of course) you could use the "relative" keyword, for example: write relative #0 #0 /Usersmeng/Desktop/mutations/test_22ile.pdb I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 30, 2013, at 4:35 AM, Alper Yilmaz <alperyilmaz@gmail.com> wrote:
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.
participants (3)
-
Aldo Segura -
Alper Yilmaz -
Elaine Meng