Hi, Do you know if chimera can do energy calculation? I have a protein I want to mutate some residues and calculate the energy difference before and after the mutation. Do you know if I can do that in chimera? Thanks, Bobo 发自我的 iPhone
Hi Bobo, I think Chimera does not have such capability. I would suggest you trying with FoldX: foldx.crg.es Best, Aldo 2014-10-07 17:04 GMT-04:00 <bobo2412@gmail.com>: Hi, Do you know if chimera can do energy calculation? I have a protein I want to mutate some residues and calculate the energy difference before and after the mutation. Do you know if I can do that in chimera? Thanks, Bobo 发自我的 iPhone _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users -- ========================================= Aldo Segura-Cabrera Research Fellow Division of Experimental Hematology and Cancer Biology Cancer and Blood Diseases Institute Cincinnati Children's Hospital Medical Center 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229 e-mail: Aldo.Segura-Cabrera@cchmc.org; aldosegura@gmail.com =========================================
Hi Bobo, Aldo is exactly right. You want something like a free-energy calculation or estimation, which Chimera does not do. Besides the tool Aldo mentioned, I've also heard of SDM <http://mordred.bioc.cam.ac.uk/sdm/sdm.php> , but I haven't tried either of them myself. Best, 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 Oct 7, 2014, at 3:53 PM, Aldo Segura <aldosegura@gmail.com> wrote:
Hi Bobo, I think Chimera does not have such capability. I would suggest you trying with FoldX: foldx.crg.es Best, Aldo
2014-10-07 17:04 GMT-04:00 <bobo2412@gmail.com>: Hi, Do you know if chimera can do energy calculation? I have a protein I want to mutate some residues and calculate the energy difference before and after the mutation. Do you know if I can do that in chimera? Thanks, Bobo
Thanks, I will try the programs you suggested. Bobo On Tue, Oct 7, 2014 at 6:46 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Bobo, Aldo is exactly right. You want something like a free-energy calculation or estimation, which Chimera does not do.
Besides the tool Aldo mentioned, I've also heard of SDM < http://mordred.bioc.cam.ac.uk/sdm/sdm.php> , but I haven't tried either of them myself. Best, 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 Oct 7, 2014, at 3:53 PM, Aldo Segura <aldosegura@gmail.com> wrote:
Hi Bobo, I think Chimera does not have such capability. I would suggest you trying with FoldX: foldx.crg.es Best, Aldo
2014-10-07 17:04 GMT-04:00 <bobo2412@gmail.com>: Hi, Do you know if chimera can do energy calculation? I have a protein I want to mutate some residues and calculate the energy difference before and after the mutation. Do you know if I can do that in chimera? Thanks, Bobo
participants (4)
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Aldo Segura -
Bobo Dang -
bobo2412＠gmail.com
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Elaine Meng