atomworks/CITATION.cff at production · RosettaCommons/atomworks · GitHub

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cff-version: 1.2.0
title: atomworks
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - family-names: Corley
    given-names: Nathaniel
  - family-names: Mathis
    given-names: Simon
  - family-names: Krishna
    given-names: Rohith
  - family-names: Bauer
    given-names: Magnus S.
  - family-names: Thompson
    given-names: Tuscan R.
  - family-names: Ahern
    given-names: Woody
  - family-names: Kazman
    given-names: Maxwell W.
  - family-names: Brent
    given-names: Rafael I.
  - family-names: Didi
    given-names: Kieran
  - family-names: Kubaney
    given-names: Andrew
  - family-names: McHugh
    given-names: Liam
  - family-names: Nagle
    given-names: Andrew
  - family-names: Favor
    given-names: Adam
  - family-names: Kshirsagar
    given-names: Meghana
  - family-names: Sturmfels
    given-names: Pascal
  - family-names: Li
    given-names: Yinuo
  - family-names: Butcher
    given-names: John
  - family-names: Qiang
    given-names: Bo
  - family-names: Schaaf
    given-names: Luna L.
  - family-names: Mitra
    given-names: Ria
  - family-names: Campbell
    given-names: Kerrie
  - family-names: Zhang
    given-names: Opa
  - family-names: Weissman
    given-names: Rose
  - family-names: Humphreys
    given-names: Ian R.
  - family-names: Cong
    given-names: Qian
  - family-names: Jiang
    given-names: Hanlun
  - family-names: Funk
    given-names: Jason
  - family-names: Sonthalia
    given-names: Satyaki
  - family-names: Lio
    given-names: Pietro
  - family-names: Baker
    given-names: David
  - family-names: DiMaio
    given-names: Frank
identifiers:
  - type: doi
    value: 10.1101/2025.08.14.670328
    description: bioRxiv preprint
repository-code: https://github.com/RosettaCommons/atomworks
url: https://rosettacommons.github.io/atomworks/latest/
abstract: >-
  A research-oriented data toolkit for training biomolecular
  deep-learning foundation models. AtomWorks provides tools
  for parsing, cleaning, manipulating, and converting
  biological data (structures, sequences, small molecules)
  as well as advanced dataset featurization and sampling for
  deep learning workflows.
keywords:
  - bioinformatics
  - machine-learning
  - deep-learning
  - protein-structure
  - biotite
  - structural-biology
license: BSD-3-Clause