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Questions and answers => General discussions (Q&As) => Topic started by: adolfo on January 21, 2020, 07:11:45 am

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Title: runing x3dna for CG dna structure (without base-pairing information)
Post by: adolfo on January 21, 2020, 07:11:45 am
Dear all,
I am new in this community. Here my question, will it be possible get global helical parameters (e.g. mino/major groove, pitch, rise,..) for a coarse grained double-helix DNA structure using only the P atoms for each residue?
Thanks for your help!
Adolfo
Title: Re: runing x3dna for CG dna structure (without base-pairing information)
Post by: xiangjun on January 21, 2020, 09:29:23 am
Hi Adolfo,

Thanks for joining the 3DNA/DSSR user community, and for posting your question on the Forum.

Quote
will it be possible get global helical parameters (e.g. mino/major groove, pitch, rise,..) for a coarse grained double-helix DNA structure using only the P atoms for each residue?

The answer is no. 3DNA/DSSR requires base atoms to deduce base types and pairs etc. Please check for a utility that converts P-only coarse-grained models to full atomic models. It helps if you could share your findings for the community.

Best regards,

Xiang-Jun
Title: Re: runing x3dna for CG dna structure (without base-pairing information)
Post by: adolfo on January 23, 2020, 03:49:49 am
Dear Xiang-Jun,
thanks for your response. Could you share some steps to the utility in 3DNA which can take P atoms (see 22 CG B-DNA structure in attachment) and reconstruct a full atomistic structure based on a CG model. I would really appreciate some help as the wDNA does not support such right away structure loading.
best,
adolfo
Title: Re: runing x3dna for CG dna structure (without base-pairing information)
Post by: xiangjun on January 23, 2020, 10:32:39 am
Hi Adolfo,

As mentioned in my initial response, 3DNA/DSSR (and the 3DNA 2.0 web server) does not have the means to convert a coarse-gained (CG) model to an full-atomic 3D structure: 3DNA/DSSR requires base atoms to deduce base types and pairs etc. Maybe it was not that clear, I was suggesting that you check somewhere else for such a utility. Presumably, the resources that produce the CG model should have such options.

A quick Google search led to "Reconstruction of Atomistic Structures from Coarse-Grained Models for Protein–DNA Complexes (https://doi.org/10.1021/acs.jctc.7b00954)". However, it reconstructs atomic details of DNA structures from a three-site per nucleotide CG model. Nevertheless, searching along the line, I'm almost certain there must be an already existing approach that convert P-only CG models to full-atomic models.

Also, posting this question to the CG-modeling community is more likely to get a concrete answer.

Best regards,

Xiang-Jun

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.