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deepchem / openstone

An experimental package for open source algorithms for computational modeling and analysis of protein structures.
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Openstone ideas #1

Open rbharath opened 4 years ago

rbharath commented 4 years ago

Rosetta is a unique and powerful piece of software, but it appears like there isn't a current open source equivalent (discussion). I'm starting this repo to begin building towards such a project. The name, openstone is a play on the Rosetta stone. Rosetta is a large and sophisticated piece of software, so it's unlikely that initial versions of this project will have anywhere near the same functionality, but here are some of the things I'd like to eventually support:

To the degree possible, we should lean on other open source toolkits. I think OpenMM, pdbfixer, rdkit could be used to do a lot of the molecular heavy lifting. TensorFlow or PyTorch could be used to provide learning capabilities.

For now, this repo is going to be a stub, but let's use this thread to brainstorm some architecture and design ideas.

rbharath commented 4 years ago

Modeller is another powerful piece of software that allows for homology modeling. I'm not sure if there's a good way to homology model with open source tools. Perhaps with biopython?

rbharath commented 4 years ago

https://github.com/graik/biskit is a open source GPL python package for structural bioinformatics that could be a neat resource.