Dear Chimera Users, I am studying on aprotein and its interactions with its ligands and I want to explore what wouldbe the effect on protein thermodynamic stability if some parameters were changed such asaddition, removal of hydrogen bonds or other forces. Any idea on how to dothat? I am new on this. Thank you on advance! Kloe
Hi Kloe, Chimera does not calculate free energies or thermodynamic stabilities, sorry. This generally requires much more extensive modeling, such as long dynamics simulations with a dedicated package like AMBER, Gromacs, etc. Other, more empirical programs (i.e. easier to use and shorter calculations) also exist for estimating the effects on stability of mutations, but I don’t have specific knowledge or recommendations in that area. What you can do with Chimera is simple first-order assessments of amino acid mutations or modifications of ligands, by simply counting up H-bonds and steric clashes, or performing small local minimizations, and using your own chemical intuition. I hope this clarifies the situation, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2018, at 10:42 AM, kloe brathon <kloebrathon@yahoo.com> wrote:
Dear Chimera Users, I am studying on a protein and its interactions with its ligands and I want to explore what would be the effect on protein thermodynamic stability if some parameters were changed such as addition, removal of hydrogen bonds or other forces. Any idea on how to do that? I am new on this. Thank you on advance! Kloe
Thank you for the reply! I do not need many specifities. I only need to imagine what could be the change. Can I please have any more information or any website where I can learn the steps to perform local minimization/ count steric clashes/H bonding in Chimera?I do not know where to start from. I would highly appreciate any clue. Thank you! Kloe Sent from Yahoo Mail for iPhone On Friday, December 21, 2018, 9:59 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Kloe, Chimera does not calculate free energies or thermodynamic stabilities, sorry. This generally requires much more extensive modeling, such as long dynamics simulations with a dedicated package like AMBER, Gromacs, etc. Other, more empirical programs (i.e. easier to use and shorter calculations) also exist for estimating the effects on stability of mutations, but I don’t have specific knowledge or recommendations in that area. What you can do with Chimera is simple first-order assessments of amino acid mutations or modifications of ligands, by simply counting up H-bonds and steric clashes, or performing small local minimizations, and using your own chemical intuition. I hope this clarifies the situation, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2018, at 10:42 AM, kloe brathon <kloebrathon@yahoo.com> wrote:
Dear Chimera Users, I am studying on a protein and its interactions with its ligands and I want to explore what would be the effect on protein thermodynamic stability if some parameters were changed such as addition, removal of hydrogen bonds or other forces. Any idea on how to do that? I am new on this. Thank you on advance! Kloe
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Hi Kloe, There are many tutorials, including “Getting Started” for new users, “Structure Analysis and Comparison” for examples of finding H-bonds and clashes, etc. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> For general information of what’s available, you can look at the User’s Guide, which lists all the tools and commands with short descriptions of each: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html> Open tools from the Chimera Tools menu, for example: Tools… Structure Analysis… FindHBond Tools… Structure Analysis… Find Clashes/Contacts Tools… Structure Editing… Minimize Structure Not everything is included in some tutorial, but if you click the Help button on each tool it will show the full description of that tool and its options. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2018, at 11:31 AM, Xhoela Bame <xhoelabame@yahoo.com> wrote:
Thank you for the reply! I do not need many specifities. I only need to imagine what could be the change. Can I please have any more information or any website where I can learn the steps to perform local minimization/ count steric clashes/H bonding in Chimera? I do not know where to start from. I would highly appreciate any clue. Thank you! Kloe
On Friday, December 21, 2018, 9:59 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Kloe, Chimera does not calculate free energies or thermodynamic stabilities, sorry. This generally requires much more extensive modeling, such as long dynamics simulations with a dedicated package like AMBER, Gromacs, etc. Other, more empirical programs (i.e. easier to use and shorter calculations) also exist for estimating the effects on stability of mutations, but I don’t have specific knowledge or recommendations in that area.
What you can do with Chimera is simple first-order assessments of amino acid mutations or modifications of ligands, by simply counting up H-bonds and steric clashes, or performing small local minimizations, and using your own chemical intuition. I hope this clarifies the situation, Elaine
Thank you very much for the reply! Happy feasts! Kloe 21 Aralık 2018 Cuma 23:04:39 GMT+3 tarihinde, Elaine Meng <meng@cgl.ucsf.edu>şunu yazdı: Hi Kloe, There are many tutorials, including “Getting Started” for new users, “Structure Analysis and Comparison” for examples of finding H-bonds and clashes, etc. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html> <https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html> For general information of what’s available, you can look at the User’s Guide, which lists all the tools and commands with short descriptions of each: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html> Open tools from the Chimera Tools menu, for example: Tools… Structure Analysis… FindHBond Tools… Structure Analysis… Find Clashes/Contacts Tools… Structure Editing… Minimize Structure Not everything is included in some tutorial, but if you click the Help button on each tool it will show the full description of that tool and its options. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 21, 2018, at 11:31 AM, Xhoela Bame <xhoelabame@yahoo.com> wrote:
Thank you for the reply! I do not need many specifities. I only need to imagine what could be the change. Can I please have any more information or any website where I can learn the steps to perform local minimization/ count steric clashes/H bonding in Chimera? I do not know where to start from. I would highly appreciate any clue. Thank you! Kloe
On Friday, December 21, 2018, 9:59 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Kloe, Chimera does not calculate free energies or thermodynamic stabilities, sorry. This generally requires much more extensive modeling, such as long dynamics simulations with a dedicated package like AMBER, Gromacs, etc. Other, more empirical programs (i.e. easier to use and shorter calculations) also exist for estimating the effects on stability of mutations, but I don’t have specific knowledge or recommendations in that area.
What you can do with Chimera is simple first-order assessments of amino acid mutations or modifications of ligands, by simply counting up H-bonds and steric clashes, or performing small local minimizations, and using your own chemical intuition. I hope this clarifies the situation, Elaine
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participants (3)
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Elaine Meng -
kloe brathon -
Xhoela Bame