How to identify the flexible amino acids in a protein ?

zako · 发表于 Post on 2021-2-22 23:46:19

Hey everyone, how is it going?
Flexible docking always brought problems for researchers.
I wonder if there is some rules to identify flexible amino acids, and what's the best program to perform this kind of docking, because i think Autodock4 and Autodock Vina are limited.
Taking my case as an an example, after i prepared a protein (removing water molecules, Add Hydrogens and Charges) downloaded from rcsb, and i used an online server to identify the active site, which gave me 29 amino acids in the best active site . I thought that i can make all the 29 amino acids as flexibles, but it was a stupid idea.
I hope that you can assiste me in this matter.

Many thanks in advance

sobereva · 发表于 Post on 2021-2-23 00:01:36

A possible way is performing molecular dynamics, then plot superposition map of multiple frames in VMD to check which residues show significant flexibility during the simulation.

zako · 发表于 Post on 2021-2-23 01:57:22

sobereva 发表于 2021-2-23 00:01
A possible way is performing molecular dynamics, then plot superposition map of multiple frames in V ...

Thank you very much for your nice reply, but unfortunately, i haven't the necessary experience to perform MD simulation, i'm still trying to learn MD simulations using Gromacs from your amazing tutorials.
Could you advice me with another technic to reach my goal.

sobereva · 发表于 Post on 2021-2-23 10:22:13

zako 发表于 2021-2-23 01:57
Thank you very much for your nice reply, but unfortunately, i haven't the necessary experience t ...

MD is the best choice. Unfortunately, according to my knowledge, there is no other viable and easier way.

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