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google-deepmind / deepmind-research

This repository contains implementations and illustrative code to accompany DeepMind publications
Apache License 2.0
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AlphaFold folding pipeline #47

Closed Lorenzo360 closed 4 years ago

Lorenzo360 commented 4 years ago

How can you obtain the final (folded) protein 3D structure from the distance map/distogram? In the README it says:

pasted/: Contains distograms obtained from the ensembled distograms by pasting. An RR contact map file is computed from this pasted distogram. This is the final distogram that was used in the subsequent AlphaFold folding pipeline in CASP13

But where is this AlphaFold folding pipeline? If this pipeline is not published, are there alternatives? I did not find a satisfactory solution yet.

Augustin-Zidek commented 4 years ago

Unfortunately, the actual folding pipeline is not open-sourced. However, the Methods section in the AlphaFold Nature paper (https://rdcu.be/b0mtx) should provide sufficient amount of details to enable reimplementation.

monkollek commented 3 years ago

@Lorenzo360 if you are interested I implemented the protein folding part of the pipeline during the holiday break. https://github.com/leklab/alphafoldv1 as I was interested in reproducing (or close to it) for some of the figures in the Nature publication.