Datasets:

RosettaCommons
/

MIP

language: en
license: cc-by-4.0
tags:
  - chemistry
  - biology
pretty_name: Microbiome Immunity Project Protein Universe
dataset_summary: >-
  ~200,000 predicted structures for diverse protein sequences from 1,003
  representative genomes across the microbial tree of life and annotate them
  functionally on a per-residue basis.
dataset_description: >-
  Large-scale structure prediction on representative protein domains from the
  Genomic Encyclopedia of Bacteria and Archaea (GEBA1003) reference genome
  database across the microbial tree of life. From a non-redundant GEBA1003 gene
  catalog protein sequences without matches to any structural databases and
  which produced multiple-sequence alignments of N_eff > 16 and all putative
  novel domains between 40 and 200 residues were extracted. For each sequence
  20,000 Rosetta de novo models and up to 5 DMPfold models were generated. The
  initial output dataset (MIP_raw) of about 240,000 models were curated to
  high-quality models comprising about 75% of the original dataset
  (MIP_curated). Functional annotations of the entire dataset were created using
  structure-based Graph Convolutional Network embeddings from DeepFRI.
acknowledgements: >-
  We kindly acknowledge the support of the IBM World Community Grid team
  (Caitlin Larkin, Juan A Hindo, Al Seippel, Erika Tuttle, Jonathan D Armstrong,
  Kevin Reed, Ray Johnson, and Viktors Berstis), and the community of 790,000
  volunteers who donated 140,661 computational years since Aug 2017 of their
  computer time over the course of the project. This research was also supported
  in part by PLGrid Infrastructure (to PS). The authors thank Hera Vlamakis and
  Damian Plichta from the Broad Institute for helpful discussions. The work was
  supported by the Flatiron Institute as part of the Simons Foundation to
  J.K.L., P.D.R., V.G., D.B., C.C., A.P., N.C., I.F., and R.B. This research was
  also supported by grants NAWA PPN/PPO/2018/1/00014 to P.S. and T.K., PLGrid to
  P.S., and NIH - DK043351 to T.V. and R.J.X.
repo: https://github.com/microbiome-immunity-project/protein_universe
citation_bibtex: |-
  @article{KoehlerLeman2023,
    title = {Sequence-structure-function relationships in the microbial protein universe},
    volume = {14},
    ISSN = {2041-1723},
    url = {http://dx.doi.org/10.1038/s41467-023-37896-w},
    DOI = {10.1038/s41467-023-37896-w},
    number = {1},
    journal = {Nature Communications},
    publisher = {Springer Science and Business Media LLC},
    author = {Koehler Leman,  Julia and Szczerbiak,  Pawel and Renfrew,  P. Douglas and Gligorijevic,  Vladimir and Berenberg,  Daniel and Vatanen,  Tommi and Taylor,  Bryn C. and Chandler,  Chris and Janssen,  Stefan and Pataki,  Andras and Carriero,  Nick and Fisk,  Ian and Xavier,  Ramnik J. and Knight,  Rob and Bonneau,  Richard and Kosciolek,  Tomasz},
    year = {2023},
    month = apr 
  }
citation_apa: >-
  Koehler Leman, J., Szczerbiak, P., Renfrew, P. D., Gligorijevic, V.,
  Berenberg, D., Vatanen, T., … Kosciolek, T. (2023).
  Sequence-structure-function relationships in the microbial protein universe.
  Nature Communications, 14(1), 2351. doi:10.1038/s41467-023-37896-w
size_categories:
  - 100k<n<1M

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