protein-structure

See https://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py and __add__, need to do the same specifically for integer offsets.

Workaround feature + (-5) instead of feature - 5, see https://twitter.com/tomeraltman/status/1473764959347638273

I've implemented low-memory attention (9670958) using an algorithm from a recent preprint (https://arxiv.org/pdf/2112.05682.pdf), enhanced a little bit with the ability to add multiple biases + batch dimensions. Lacking the JAX map & scan used in the original implementation, which I've had to replace with for loops, ours is quite a bit slower (exact figures depend heavily on the choice of chunk si

Hey,

I would propose extend list of available models by SeqVec (ELMo-based implementation) which was presented in the Modeling aspects of the language of life through transfer-learning protein sequences paper.

SeqVec model trained on UniRef50 is available at: [SeqVec-model](

Describe the solution you'd like

• inputs for chain selection as a separate .txt file
• Input as list of PDB codes (txt file) rather than PDB directory path

This issue is a roadmap for Molly.jl development. Feel free to discuss things here or submit a PR. Bear in mind that significant refactoring will probably occur as the package develops.

Low hanging fruit

Want to get involved? These issues might be the place to start:

• Speedups to the code. Both on the level of individual functions and the overall algorithm. [Getting there]
• Look over