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How to simulate protein unfolding
- fugui
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10 years 10 months ago #1641
by fugui
How to simulate protein unfolding was created by fugui
Dear all,
The protein unfolding process is very important in many areas. However, we cannot do it using current Martini force filed because of lack of the dihedral parameters for protein.
I noticed that there is a group who developed the dihedral parameters for this purpose, and they got nice result in studying protein unfolding by using their parameters. The link of this article is :http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348680/
The problem is that i do not know how to use these parameters, does anyone have experience in that.
Any suggestion is appreciated.
BW
Fugui
The protein unfolding process is very important in many areas. However, we cannot do it using current Martini force filed because of lack of the dihedral parameters for protein.
I noticed that there is a group who developed the dihedral parameters for this purpose, and they got nice result in studying protein unfolding by using their parameters. The link of this article is :http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348680/
The problem is that i do not know how to use these parameters, does anyone have experience in that.
Any suggestion is appreciated.
BW
Fugui
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- xavier
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10 years 10 months ago #1652
by xavier
Replied by xavier on topic How to simulate protein unfolding
There is unfortunately no possibilities to study folding/unfolding of proteins with the MARTINI FF, yet.
The work you mention is an a doc parameterisation of small peptides backbone flexibility that is very useful for peptide aggregation or similar applications but will not be applicable to unfolding of proteins.
We hope to have a structurally flexible protein backbone soon.
The work you mention is an a doc parameterisation of small peptides backbone flexibility that is very useful for peptide aggregation or similar applications but will not be applicable to unfolding of proteins.
We hope to have a structurally flexible protein backbone soon.
fugui wrote: Dear all,
The protein unfolding process is very important in many areas. However, we cannot do it using current Martini force filed because of lack of the dihedral parameters for protein.
I noticed that there is a group who developed the dihedral parameters for this purpose, and they got nice result in studying protein unfolding by using their parameters. The link of this article is :http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3348680/
The problem is that i do not know how to use these parameters, does anyone have experience in that.
Any suggestion is appreciated.
BW
Fugui
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