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Author Topic: Creation of customized structures using DSSR  (Read 8693 times)

Offline curiousphoton

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Creation of customized structures using DSSR
« on: October 12, 2023, 08:06:13 am »
Hello,

I am a Computer Science Master's student working at the intersection between Computer Science and Computational Chemistry.

We have an RNA sequence, and the 9 torsional angles (calculated by 3DNA v2.4) for each residue. Would it be possible to reconstruct the full-atom 3D structure of the RNA using DSSR Pro's rebuild program from just these two pieces of information - the sequence and the 9 torsional angles?

I apologize if this question is irrelevant for the forum, I wanted to confirm if DSSR Pro could satisfy our requirements before buying the license since the Pro version of the manual is not available.

Thank you.

Offline xiangjun

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Re: Creation of customized structures using DSSR
« Reply #1 on: October 12, 2023, 08:18:44 am »
Hi,

Thanks for your using 3DNA, and your inquiries about DSSR Pro.

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I apologize if this question is irrelevant for the forum, I wanted to confirm if DSSR Pro could satisfy our requirements before buying the license since the Pro version of the manual is not available.

It is directly relevant to the Forum. You are very welcome to post this question, and any more you may have.


Quote
We have an RNA sequence, and the 9 torsional angles (calculated by 3DNA v2.4) for each residue. Would it be possible to reconstruct the full-atom 3D structure of the RNA using DSSR Pro's rebuild program from just these two pieces of information - the sequence and the 9 torsional angles?

No, at least for now, even though it is not clear to me what exactly are the 9 torsional angles you refer to. DSSR employs 6 rigid-body parameters to quantity the relative spatial geometry between two bases (or base pairs) and uses them to build 3D models with approximate backbones. I have long been interested in adding more modeling features to DSSR ...

Best regards,

Xiang-Jun


Offline curiousphoton

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Re: Creation of customized structures using DSSR
« Reply #2 on: October 12, 2023, 08:28:21 am »
Hi,

By the 9 torsional angles, I meant the torsional and pseudotorsional angles - alpha, beta, gamma, delta, chi, epsilon, zeta, eta, theta - calculated by 3DNA's `analyze` program.

DSSR would indeed benefit from more modeling features! I'll be following the release notes to see if this particular modeling feature is ever introduced to DSSR.

Thank you for your work on this wonderful program!

Offline xiangjun

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Re: Creation of customized structures using DSSR
« Reply #3 on: October 12, 2023, 08:50:01 am »
Thanks for your follow-up.

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By the 9 torsional angles, I meant the torsional and pseudotorsional angles - alpha, beta, gamma, delta, chi, epsilon, zeta, eta, theta - calculated by 3DNA's `analyze` program.

Among the 9 torsion angles, only the first 7 are independent. The last two, eta and theta, could in principle be deduced from (alpha, beta, gamma, delta, epsilon, zeta). I vaguely remember reading about software tools of building nucleic acid structures using backbone torsion angles, including only eta and theta. I just do not know how useable they are from a general user's perspective.

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DSSR would indeed benefit from more modeling features! I'll be following the release notes to see if this particular modeling feature is ever introduced to DSSR.

If you have info in modeling nucleic acids, please share them along this thread. I appreciate your kind words on DSSR.

Best regards,

Xiang-Jun


Offline curiousphoton

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Re: Creation of customized structures using DSSR
« Reply #4 on: October 12, 2023, 10:00:12 am »
Quote
I vaguely remember reading about software tools of building nucleic acid structures using backbone torsion angles, including only eta and theta. I just do not know how useable they are from a general user's perspective.

Oh wow! No issues with their usability, I will try to figure them out. Please let me know if you ever remember the names of these software tools.

And yes, I will share any comments or suggestions I have about modelling in this thread when I think of any.

Offline xiangjun

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Re: Creation of customized structures using DSSR
« Reply #5 on: October 12, 2023, 11:06:59 am »
Have a look at "The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs" (https://academic.oup.com/nar/article/49/1/79/6029180):

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"To aid the development of novel XNA polymers and the search for possible pre-RNA candidates, this article presents the proto-Nucleic Acid Builder (https://github.com/GT-NucleicAcids/pnab), an open-source program for modeling nucleic acid analogs with alternative backbones and nucleobases. The torsion-driven conformation search procedure implemented here predicts structures with good accuracy compared to experimental structures, and correctly demonstrates the correlation between the helical structure and the backbone conformation in DNA and RNA."

Please report back how it goes.

Best regards,

Xiang-Jun

Offline xiangjun

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Re: Creation of customized structures using DSSR
« Reply #6 on: October 12, 2023, 11:11:25 am »
Also "RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2317-9):

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Here, we present RNAfitme, a versatile webserver tool for remodeling of nucleobase- and nucleoside residue conformations in the fixed-backbone RNA 3D structures. Our approach makes use of dedicated libraries that define RNA conformational space. They have been built upon torsional angle characteristics of PDB-deposited RNA structures. RNAfitme can be applied to reconstruct full-atom model of RNA from its backbone; remodel user-selected nucleobase/nucleoside residues in a given RNA structure; predict RNA 3D structure based on the sequence and the template of a homologous molecule of the same size; refine RNA 3D model by reducing steric clashes indicated during structure quality assessment. RNAfitme is a publicly available tool with an intuitive interface. It is freely accessible at http://rnafitme.cs.put.poznan.pl/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.