Protein structure network analysis of a peptide ensemble with Bio3D R package (Advanced)

This is a slightly advanced tutorial which will guide you to perform Dynamic Cross-Correlation Network Analysis on a predominantly disordered ensemble of the IDP amyloid-beta 42 using the R statistical computing package Bio3D.
www.r-project.org
thegrantlab.org...

[@wesam4470]

very good and detailed tutorial! Could you please share the R scripts (path_analysis.R and dccm.R)? Thanks!

[@1980yadalam]

very useful video. thanks.

[@aasukhan3635]

​ @shayonbh_molmod hi can you please let me know how can i perform cross-correlation for a complex a receptor with small molecule ligand. as ligand has only one residue and donot contain CA . thank you.

[@rahulmakkad3910]

Hi Shayon, Amazing video, all well explained. Thanks for making this video. Can you please make such a detailed video on PCA?
Ritu

[@shayonbh_molmod]

Thanks Ritu! I can't promise when, but I might do it at some point.. do you mean PCA via Bio3D?

[@rahulmakkad3910]

@@shayonbh_molmod Yes, I meant PCA using bio3D. Btw which program do you prefer for performing Cartesian or dihedral PCA.

[@shayonbh_molmod]

@@rahulmakkad3910 I usually end up writing my own code for variants of PCA if needed, but Bio3D is very good too for Cartesian PCA!

[@hitkarshkushwaha2434]

Please Make a tutorial on complete MD Simulation..

[@shayonbh_molmod]

There are few great tutorial links on complete MD simulations already. Please have a look at this one with Gromacs: th-cam.com/video/rYZ1p5lXNyc/w-d-xo.html

[@ikponwmosaobaseki3645]

Plz can you share the scripts thank you

[@muhammadrezkirasyak]

i hope that you kindly share the R code sir, or your gituhub which posted about this code