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Author Topic: Adding missing residue in PDB file of RNA  (Read 1678 times)

Offline sunil10654

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Adding missing residue in PDB file of RNA
« on: February 08, 2017, 11:09:32 am »
Hello Everyone,


I have a PDB file for RNA. Co-ordinates of 8 nucleotide residues are missing in the pdb file. I know the missing sequence of residues. I need the co-ordinates of complete RNA sequence. Can I add the missing residue and create a modified PDB file of complete sequence using x3DNA ?


Sequence :  GGGCUUCGUUAGGUGAGGCUCCUGUAUGGAGAUACGCUGCUGCCCAAAAAUGUCCAAAGACGCCAAUGGGUCAACAGAAA
UCAUCGACAUAAGGUGAUUUUUAAUGCAGCUGG--(AUGCUUGU)--CCUAUGCCAUACAGUGCUAAAGCUCUACGAUUGAAGCCCA

The region in bracket is missing in PDB file.

Requirement : PDB file of complete sequence.
Thanks.
« Last Edit: February 08, 2017, 11:12:31 am by sunil10654 »

Offline xiangjun

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Re: Adding missing residue in PDB file of RNA
« Reply #1 on: February 08, 2017, 11:25:46 am »
Hi,

I understand what you mean. Unfortunately, 3DNA currently do not have the direct means to fit your need. The rebuild and mutate_bases programs in 3DNA all need a starting structure to manipulate. RNA model building, like in your case, is an area of future direction of 3DNA.

You may find NAB from the Case group useful. There are also some other dedicated RNA modeling tools, as shown in RNA-Puzzles. Please let us know how things go.

Best regards,

Xiang-Jun
« Last Edit: February 08, 2017, 11:27:58 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline sunil10654

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Re: Adding missing residue in PDB file of RNA
« Reply #2 on: February 08, 2017, 11:30:00 am »
Dear xiangjun,

Thanks for your reply and concern.
This is a great platform to use.
Best of luck for your future endeavor.

Offline xiangjun

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Re: Adding missing residue in PDB file of RNA
« Reply #3 on: February 08, 2017, 11:38:03 am »
Hi,

Thanks for your kind words. If possible, please share you experience in solving the problem you posted. 3DNA may be useful at certain stage(s) of the process, if you fail to find a fully automated way that perfectly does the trick.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.