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MP-NeRF: A Massively Parallel Method for Accelerating Protein Structure Reconstruction from Internal Coordinates

View ORCID ProfileEric Alcaide, View ORCID ProfileStella Biderman, View ORCID ProfileAmalio Telenti, View ORCID ProfileM. Cyrus Maher
doi: https://doi.org/10.1101/2021.06.08.446214
Eric Alcaide
1Vir Biotechnology Inc., San Francisco, California, 94158, USA
2EleutherAI, Fully Online:
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  • For correspondence: ealcaide@vir.bio cmaher@vir.bio
Stella Biderman
2EleutherAI, Fully Online:
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Amalio Telenti
1Vir Biotechnology Inc., San Francisco, California, 94158, USA
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M. Cyrus Maher
1Vir Biotechnology Inc., San Francisco, California, 94158, USA
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  • For correspondence: ealcaide@vir.bio cmaher@vir.bio
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Abstract

The conversion of proteins between internal and cartesian coordinates is a limiting step in many pipelines, such as molecular dynamics simulations and machine learning models. This conversion is typically carried out by sequential or parallel applications of the Natural extension of Reference Frame (NeRF) algorithm. This work proposes a massively parallel NeRF implementation which, depending on the polymer length, achieves speedups between 400-1200x over the previous state-of-the-art. It accomplishes this by dividing the conversion into three main phases: parallel composition of the monomer backbone, assembly of backbone subunits, and parallel elongation of sidechains; and by batching these computations into a minimal number of efficient matrix operations. Special emphasis is placed on reusability and ease of use. We open source the code (available at https://github.com/EleutherAI/mp_nerf) and provide a corresponding python package.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/EleutherAI/mp_nerf

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 09, 2021.
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MP-NeRF: A Massively Parallel Method for Accelerating Protein Structure Reconstruction from Internal Coordinates
Eric Alcaide, Stella Biderman, Amalio Telenti, M. Cyrus Maher
bioRxiv 2021.06.08.446214; doi: https://doi.org/10.1101/2021.06.08.446214
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MP-NeRF: A Massively Parallel Method for Accelerating Protein Structure Reconstruction from Internal Coordinates
Eric Alcaide, Stella Biderman, Amalio Telenti, M. Cyrus Maher
bioRxiv 2021.06.08.446214; doi: https://doi.org/10.1101/2021.06.08.446214

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