Tools to be checked

[dprada]

Some tools that should be checked, either because they could be useful for MolSysMT, or because they have a similar purpose.

[dprada]

Info dumped here to be reviewed by the author soon

https://molmod.ugent.be/software

Engines and classes to be included

PyPDB
https://academic.oup.com/bioinformatics/article/32/1/159/1743800
Biopython
https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
PyRosetta
Modeller (from openmm)

Files formats to be included

Ideas in queue

• cites_tracker(): a function to be initialized at the begining of a jupyter notebook which at any moment can print out the relevant references regarding the python libraries the user needs to cite up to that point of the notebook. [cites_tracker('reset'),cites_tracker()]

Things to be checked

https://github.com/mdyzma/md_how_to/blob/master/source/tools.rst
https://github.com/westpa/westpa/wiki/Pairing-WESTPA-with-MDAnalysis-&-MDTraj
https://github.com/MDAnalysis/mdanalysis/wiki/Examples

Libraries and Software that have to be checked

https://github.com/drorlab/atom3d
https://github.com/drorlab/pensa
https://github.com/RUBi-ZA/MD-TASK

https://opensourcemolecularmodeling.github.io/