Work

Sequence-structure-function relationships in the microbial protein universe

Year: 2022

Type: dataset

Abstract: The Microbiome Immunity Project (MIP) dataset contains models predicted with both Rosetta and DMPFold (folder `dataset/`). It also contains DeepFRI function predictions for all models. The `metadata` folder contains additional data which may be useful for searching the MIP database (FASTA files, BLAST databases and useful scripts for structure/function search) as well as retrieving the sequence/structural annotations. The `intermediate_data` folder contains preprocessed output for reproducing many of the figures in our manuscript in conjunction with scripts and Juypter notebooks found in our git repository: https://github.com/microbiome-immunity-project/protein_universe . More information about the dataset and associated metadata is provided in the `README.md` file). We are also providing workflows to search the MIP database against a protein sequence or structure or function of interest (see `SEARCHING.md` for more details).

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.6477241

Authors: Koehler Leman, Julia, Szczerbiak, Pawel, Renfrew, P. Douglas, Gligorijevic, Vladimir, Berenberg, Daniel, Vatanen, Tommi, Taylor, Bryn C., Chandler, Chris, Janssen, Stefan, Pataki, Andras, Carriero, Nick, Fisk, Ian, Xavier, Ramnik J., Knight, Rob, Bonneau, Richard, Kosciolek, Tomasz

Institutions: Simons Foundation, Flatiron Institute, Jagiellonian University, Broad Institute, University of California San Diego

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

OpenAlex ID: W4393478243

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