How to find flexible residues in a protein using MD Simulation ?

maximos · 发表于 Post on 2021-6-8 07:27:07

Hi all,
I want to perform a flexible molecular docking of some ligands, and the flexibility of the protein is very important, but i don't know how to defind the flexible residues of my protein. I did some research, and i always find that to the MD simulation is mandatory.
I have some basics in Gromacs, but i don't know how to reach my goal.
Please, if there is a tutorial about that, share it.

Many thanks in advance

hdhxx123 · 发表于 Post on 2021-6-8 08:19:23

you can try this:
gmx rmsf -f XXX.xtc -s XXX.tpr -o rmsf_protein.xvg -oq bfac.pdb -res -b A
XXX is the name of your files,A is the start frame of sampling for calculating RMSF and Beta Factor.
the Beta Factor,which is derived from rmsf,is a way to perform the flexibility of the protein.
you can import bfac.pdb into VMD ,choose "Beta" as Coloring Method,then you can get the the flexibility of residues visually.

hdhxx123 · 发表于 Post on 2021-6-8 08:26:53

If you can understand Chinese ,it's recommended to read the article of Sobereva:
http://sobereva.com/32

sobereva · 发表于 Post on 2021-6-8 19:33:31

As mentioned in #2, you can perform several nanoseconds MD simulation, and then calculate RMSF of each residue in the possible binding region. The residue with relatively large RMSF is usually flexible , and may need to be set to be flexible in your docking code.

maximos · 发表于 Post on 2021-6-24 04:54:01

Thank you All very much for your valuable answers,
During my searching in the same subject, I found an article where the authors use another method to analyse the flexibility of proteins. (Please see attached image)

Source (https://www.nature.com/articles/s41598-020-77794-5.pdf)

Could you please explain how to use this method ?

hdhxx123 · 发表于 Post on 2021-6-24 12:12:39

maximos 发表于 2021-6-24 04:54
Thank you All very much for your valuable answers,
During my searching in the same subject, I found ...

if you want to use this method,In VMD,you can choose "Extension"-"Analysis"-"RMSD Trajectory Tools".Then choose the residues you want to calculate.After choose the proper parameters,press "Align" and "RMSD".Besides,you can also use "Extension"-"Analysis"-"Timeline".
You also can do it through Gromacs,it's recommended to read the manual.

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[GROMACS] How to find flexible residues in a protein using MD Simulation ?

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