Science Score: 57.0%
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Low similarity (12.1%) to scientific vocabulary
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Repository
Ducque - Mechanical Nucleic Acid Architect
Basic Info
Statistics
- Stars: 3
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
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Metadata Files
README.md
Ducque
The model builder of choice to generate helical structures. Provides an interface for the user to supply the Ducque library with user-defined, custom chemistries so you can build virtual structures with never-seen-before molecules!
Ducque has four (4) main functions:
- --build : module to generate (X)NA helical models.
- --transmute : module to insert user-defined chemistries into Ducque's library.
- --xyz_pdb : module to convert a given xyz file to the pdb format.
- --randomise : module to randomise a sequence, used for --build .
- --gui opens the GUI to use the modules up above, instead of the CLI. The tlinker module, in the gui module, is a specific preset for implementing linker fragments.
Model building documentation
A comprehensive manual of Ducque is found inside the Ducque/docs/ directory !
Forcefield
To know more about how to build a forcefield, definitely check the Ducque/ff/ directory!
Charge derivation implementation with ORCA
All scripts to calculate point charges, according to the AMBER-compatible MK population analysis scheme, can be found in the Ducque/ff/scripts/ directory.
The How_To_Create_A_Forcefield.pdf file guides the user through the correct protocol and where to download the requires software packages.
Reference
If you've used Ducque or any of its parts, or you've used the How_To_Create_A_Forcefield.pdf as a guide for your own research, please cite the following published article :
[1] Jérôme Rihon, Charles-Alexandre Mattelaer, Rinaldo Wander Montalvão, Mathy Froeyen, Vitor Bernardes Pinheiro, Eveline Lescrinier, Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline, Nucleic Acids Research, 2024; DOI: 10.1093/nar/gkae135, https://doi.org/10.1093/nar/gkae135
bibtex
@article{Rihon_2024,
title={Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline},
volume={52},
ISSN={1362-4962},
url={http://dx.doi.org/10.1093/nar/gkae135},
DOI={10.1093/nar/gkae135},
number={6},
journal={Nucleic Acids Research},
publisher={Oxford University Press (OUP)},
author={Rihon, Jérôme and Mattelaer, Charles-Alexandre and Montalvão, Rinaldo Wander and Froeyen, Mathy and Pinheiro, Vitor Bernardes and Lescrinier, Eveline},
year={2024},
month=feb,
pages={2836–2847}
}
Authors
Jérôme Rihon (@jrihon )
Owner
- Login: jrihon
- Kind: user
- Location: Leuven, Belgium
- Company: KU Leuven
- Repositories: 2
- Profile: https://github.com/jrihon
I'm a PhD computational researcher over at the laboratory of Medicinal Chemistry at Rega Institute for Medical Research!
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: >-
Structural insights into the morpholino nucleic acid/RNA
duplex using the new XNA builder Ducque in a molecular
modeling pipeline
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Jérôme
family-names: Rihon
email: jeromerihon@gmail.com
affiliation: >-
Laboratory of Medicinal Chemistry, Rega Institute for
Medical Research, Herestraat 49, Box 1030, B-3000
Leuven, Belgium
orcid: 'https://orcid.org/0000-0002-9207-1556'
- given-names: Charles-Alexandre
family-names: Mattelaer
affiliation: >-
Quantum Chemistry and Physical Chemistry,
Celestijnenlaan 200f, Box 2404, B-3001, Leuven,
Belgium
- given-names: Rinaldo
family-names: ' Wander Montalvão'
affiliation: >-
Gain Therapeutics sucursal en España, Barcelona
Science Park, Baldiri Reixac 4-10, 08028 Barcelona,
Spain
- given-names: Mathy
family-names: Froeyen
affiliation: >-
Laboratory of Medicinal Chemistry, Rega Institute for
Medical Research, Herestraat 49, Box 1030, B-3000
Leuven, Belgium
- given-names: Vitor
family-names: Berardes Pinheiro
affiliation: >-
Laboratory of Medicinal Chemistry, Rega Institute for
Medical Research, Herestraat 49, Box 1030, B-3000
Leuven, Belgium
- given-names: Eveline
family-names: Lescrinier
email: eveline.lescrinier@kuleuven.be
orcid: 'https://orcid.org/0000-0001-7066-4329'
affiliation: >-
Laboratory of Medicinal Chemistry, Rega Institute for
Medical Research, Herestraat 49, Box 1030, B-3000
Leuven, Belgium
identifiers:
- type: doi
value: 10.1093/nar/gkae135
- type: url
value: 'https://doi.org/10.1093/nar/gkae135'
repository-code: 'https://github.com/jrihon/Ducque'
abstract: >-
The Ducque model builder to build virtual (X)NA duplexes,
for a pure in silico molecular modeling pipeline
keywords:
- Xenobiotic Nucleic Acid
- Model builder
- Structural Biology
- Cheminformatics
- Molecular Modeling
license: MIT
version: '1.0'
date-released: '2024-02-19'
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