Subject: Re: Solution structure for Protein - WorkFlow
From: woonghee_lee
Date: Jan 19, 2016

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Hi Insiya,

For a 79 residue protein, if you are experienced enough and the spectra are good, it will take less than a week if you follow the protocol that NMRFAM established. Other alternative can be applied too but I will stick with mine for now because I know the fastest way with them.

1. Picking peaks and validating them by APES. Use restricted-peak picking for HCCH-TOCSY.
https://www.youtube.com/watch?v=lMEFfJfRRIMlist=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=4


2. Submit to PINE. Try to submit backbone only one time and backbone + sidechain the other time. See the probabilities for side chain, and you think they are good mostly 80%, you use PINE results. Use PINE-SPARKY to validate them. If they are not good, use only backbone and do the superfast methods.


https://www.youtube.com/watch?v=vSlT7y5hT5glist=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=6


https://www.youtube.com/watch?v=l50CE-M1KE0list=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=8


3. Check your nomenclature and assignment confidence.

https://www.youtube.com/watch?v=I0mNdR3MHiwlist=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=30

https://www.youtube.com/watch?v=KqPstgautBElist=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=29


4. Run PONDEROSA-C/S

https://www.youtube.com/watch?v=zjO8Xh6VgV0list=PLmYqoarOFAZ-aInZ5uM2pV63e7yMSHSuZindex=14


5. Validate distance and angle constraints with Ponderosa Analyzer and PyMOL.

https://www.youtube.com/watch?v=L7vM_PrSnrglist=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=9

https://www.youtube.com/watch?v=12qKSA6Ku00list=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=10

https://www.youtube.com/watch?v=Tq7e8VK9ivElist=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=13

6. Iterate until you get reasonably good structure

https://www.youtube.com/watch?v=gqb8e_mNBk0list=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=14

7. Use final step option for large sampled structure generation


8. Validate structure quality.

https://www.youtube.com/watch?v=zPslIiR6Y1slist=PLmYqoarOFAZ9Um_2DNL6Bw-gy92VJscfWindex=18


Let me know if you need further help.


Cheers,

Woonghee