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PreprintCited by 29Genomics and Rare DiseasesProtein Structure and DynamicsEnzyme Structure and Function

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Genomics 2 Proteins portal: A resource and discovery tool for linking genetic screening outputs to protein sequences and structures

Open access
Kwon, Seulki, Safer, Jordan, Nguyen, Duyen T., Hoksza, David, May, Patrick, Arbesfeld, Jeremy A., Rubin, Alan F., Campbell, Arthur J, Burgin, Alex, Iqbal, Sumaiya·2024·Nature Methods
DOI 10.1101/2024.01.02.573913PMC PMC11466821

Preprint — published as 10.1038/s41592-024-02409-0

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Abstract

Recent advances in AI-based methods have revolutionized the field of structural biology. Concomitantly, high-throughput sequencing and functional genomics technologies have enabled the detection and generation of variants at an unprecedented scale. However, efficient tools and resources are needed to link these two disparate data types – to “map” variants onto protein structures, to better understand how the variation causes disease and thereby design therapeutics. Here we present the Genomics 2 Proteins Portal (G2P; g2p.broadinstitute.org/): a human proteome-wide resource that maps 19,996,443 genetic variants onto 42,413 protein sequences and 77,923 structures, with a comprehensive set of structural and functional features. Additionally, the G2P portal generalizes the capability of linking genomics to proteins beyond databases by allowing users to interactively upload protein residue-wise annotations (variants, scores, etc.) as well as the protein structure to establish the connection. The portal serves as an easy-to-use discovery tool for researchers and scientists to hypothesize the structure-function relationship between natural or synthetic variations and their molecular phenotype.

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Metadata

Authors
Kwon, S., Safer, J., Nguyen, D. T., Hoksza, D., May, P., Arbesfeld, J. A., Rubin, A. F., Campbell, A. J., Burgin, A., & Iqbal, S.
Affiliations
  • Broad Institute (US)
  • Charles University (CZ)
  • University of Luxembourg (LU)
  • Nationwide Children's Hospital (US)
  • The University of Melbourne (AU)
Corresponding author
Iqbal, Sumaiya
ORCID
Venue
Nature Methods
Publisher
openRxiv
Published
2024-01-02
Volume
21
Issue
10
Pages
1947-1957
ISSN
1548-7091 (ISSN-L)
DOI
10.1101/2024.01.02.573913
PMC
PMC11466821
OpenAlex
W4402634357
Cited by
29
References
1
Citations by year
2026: 15 · 2025: 11 · 2024: 3
FWCI
7.66
Type
journal article
Language
en
Open access
Licence
cc-by-nc-nd
Locations
  • Nature Methods (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • Open Repository and Bibliography (University of Luxembourg) (submittedVersion, public-domain)
  • PubMed Central (submittedVersion)
  • Minerva Access (University of Melbourne) (submittedVersion, cc-by-nc-nd)
Funders
  • U.S. Department of Health and Human Services (RM1HG010461, UM1HG011969)
  • Broad Institute
  • Australian Government
  • National Institutes of Health
  • National Human Genome Research Institute (RM1HG010461, UM1HG011969)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Keywords
genetic variants, protein structure, protein sequences, structure-function relationship, human proteome, variant annotation, pathogenic variants

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