Not issue, but rather a request for information

[Nanobioinformatician]

Hello!

I have a request, “Conformer plot. Each point represents a structure with point color indicating the membership ID of the clustering. Three major clusters or groups are identified: Group 1 (black) representing inactive GPCR structures, Group 2 (red) representing active GPCR structures, and Group 3 (green).” how we identify active, inactive and how about green?

Could this cluster also be applicable to essential dynamics of MD traj analysis to identify active and inactive conformers?

I would appreciate your reply as I read tutorials but I could not find the required information!

Best

SvB

[Xinqiu Yao]

Hi,

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Whether it is “active” or “inactive” is a judgment based on prior knowledge about the system. The clustering itself does not tell function, only structural similarity. You need to look into those clusters, focus on some representative structures for example, and decide what functional state they represent based on your knowledge. You can also use some reference PDBs (with well-known functional annotations) to label the clusters.

To my knowledge, essential dynamics is the same as PCA and so, yes, you can do it in essential dynamics as well.

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[Nanobioinformatician]

Hello~

Thanks for your response!

One more query in the same string, please, how to identify the conformer for the data point in the PCA plot as mentioned in the attached figure.

I would once again thank you and the bio3d team!

P.S. I am looking forward to the implementation of free energy surface analysis and trajectory analysis of other biomolecules, DNA and RNA, under the Bio3D package.

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