Ducque

Ducque has four (4) main functions:

• --build : the nucleic acid builder
• --transmute : converts a given pdb file to the correct json format.
• --xyz_pdb : converts a given xyz file to the proper pdb format.
• --randomise : returns a randomised sequence to the user.
• --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

@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 )