Hello,
I am new to chimerax. For my protein of interest, there is no PDB available, thus, I chose a similar protein. However, the amino acid sequence is different. Is it possible to change the amino acid structure in chimerax? Will this change the 3D conformation? If this does not work what would be a good solution for my problem?
Thanks, Peter
Hi Peter, You can change an amino acid in a protein structure from one type to another with the "swapaa" command. However, it's simply a sidechain replacement to let you do a first-order assessment of the possible effect (e.g. on local H-bonds or steric conflicts) and will not move or change any other atoms of the structure.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html
You can also do a full-scale comparative modeling of a target protein via the Modeller web service (called from within ChimeraX) using the known protein structure as the template. This requires registering at the Modeller web site to get a license key, which is free for academics. You would also need a sequence alignment opened in ChimeraX (e.g. from Blast Protein or from a file you made in some other program) of the template and target sequence. See "Modeller Comparative" tool or command:
http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/modeller.html#comparative
This can also be used to model multiprotein complexes, as in this example on our "feature highlights" page: http://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller
Of course, there are dozens of programs and web services other than ChimeraX for protein structure and/or mutation effect prediction, so it may be worth investigating the alternatives depending on the needs of your project. I don't have comprehensive knowledge on these so I couldn't give a specific recommendation.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 8, 2020, at 2:11 PM, Peter Steinhagen BA42_md21@outlook.de wrote:
Hello, I am new to chimerax. For my protein of interest, there is no PDB available, thus, I chose a similar protein. However, the amino acid sequence is different. Is it possible to change the amino acid structure in chimerax? Will this change the 3D conformation? If this does not work what would be a good solution for my problem? Thanks, Peter
Hi Elaine,
thanks for your reply. I will try your suggestions.
Best, Peter
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From: Elaine Mengmailto:meng@cgl.ucsf.edu Sent: Sunday, August 9, 2020 12:13 PM To: Peter Steinhagenmailto:BA42_md21@outlook.de Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] chimerax amino acid sequence Importance: High
Hi Peter, You can change an amino acid in a protein structure from one type to another with the "swapaa" command. However, it's simply a sidechain replacement to let you do a first-order assessment of the possible effect (e.g. on local H-bonds or steric conflicts) and will not move or change any other atoms of the structure.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html
You can also do a full-scale comparative modeling of a target protein via the Modeller web service (called from within ChimeraX) using the known protein structure as the template. This requires registering at the Modeller web site to get a license key, which is free for academics. You would also need a sequence alignment opened in ChimeraX (e.g. from Blast Protein or from a file you made in some other program) of the template and target sequence. See "Modeller Comparative" tool or command:
http://rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/modeller.html#comparative
This can also be used to model multiprotein complexes, as in this example on our "feature highlights" page: http://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller
Of course, there are dozens of programs and web services other than ChimeraX for protein structure and/or mutation effect prediction, so it may be worth investigating the alternatives depending on the needs of your project. I don't have comprehensive knowledge on these so I couldn't give a specific recommendation.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 8, 2020, at 2:11 PM, Peter Steinhagen BA42_md21@outlook.de wrote:
Hello, I am new to chimerax. For my protein of interest, there is no PDB available, thus, I chose a similar protein. However, the amino acid sequence is different. Is it possible to change the amino acid structure in chimerax? Will this change the 3D conformation? If this does not work what would be a good solution for my problem? Thanks, Peter
participants (2)
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Elaine Meng
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Peter Steinhagen