Computing Rate constant-Reg.

Sunil Tripathi

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Jun 21, 2023, 11:50:56 AM6/21/23

to browndye-users-l

Dear Browndye users,

I am a new user of Brownian Dynamics using BrownDye software. I followed the tutorial and was able to run the simulation.

I am interested to compute association and dissociation (Kon and Koff) rate constants.

I used the compute_rate_constant command to compute the association rate constant (Kon).

My question is how do calculate the dissociation rate constant (Koff)?

It would be a great help.

Thank you very much.

Best Regards,

Sunil

Gary Huber

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Jun 21, 2023, 1:46:37 PM6/21/23

to Sunil Tripathi, browndye-users-l

Hi, Sunil,

At this point, Browndye only computes Kon. We are working to put in the ability to compute off-rates. There is a software package, SEEKR (https://bio.tools/seekr), that make use of both BD and MD to compute on-rates and off-rates.

Best regards,

Gary

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Lane Votapka

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Jun 21, 2023, 2:35:43 PM6/21/23

to Gary Huber, Sunil Tripathi, browndye-users-l

Hi Sunil,

It looks like that SEEKR link that Gary shared might be broken. We recommend all users to use SEEKR2, which can be found at https://github.com/seekrcentral/seekr2.git, along with instructions and tutorials.

Thanks for the recommendation, Gary!

-Lane

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Lane Votapka Ph.D.

Staff Scientist, Amaro lab

UC San Diego

Sunil K Tripathi

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Jun 21, 2023, 4:56:39 PM6/21/23

to Lane Votapka, Gary Huber, browndye-users-l

Dear Gary and Lane,

Thank you both for your valuable suggestions. I will go ahead accordingly.

Best Regards,

Sunil

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