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Cited by 0Genomics and Rare DiseasesEnzyme Structure and FunctionProtein Structure and Dynamics

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3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures

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Ruiz-Serra, Victoria, Valentini, Samuel, Madroñero, Sergi, Valencia, Alfonso, Porta-Pardo, Eduard·2024·Bioinformatics
DOI 10.1093/bioinformatics/btae171PMC PMC11018535

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Abstract

Motivation: The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional context to genetic coding variants. However, mapping genes to proteins is a tedious and error-prone task due to inconsistencies in data formats. Over the past two decades, numerous tools and databases have been developed to automatically map annotated positions and variants to protein structures. However, most of these tools are web-based and not well-suited for large-scale genomic data analysis. Results: To address this issue, we introduce 3Dmapper, a stand-alone command-line tool developed in Python and R. It systematically maps annotated protein positions and variants to protein structures, providing a solution that is both efficient and reliable. Availability and implementation: https://github.com/vicruiser/3Dmapper

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Metadata

Authors
Ruiz-Serra, V., Valentini, S., Madroñero, S., Valencia, A., & Porta-Pardo, E.
Affiliations
  • Barcelona Supercomputing Center (BSC)
  • University of Trento (IT)
  • Josep Carreras Leukaemia Research Institute (ES)
  • Institució Catalana de Recerca i Estudis Avançats (ES)
ORCID
Venue
Bioinformatics
Publisher
Oxford University Press (OUP)
Published
2024-03-29
Volume
40
Issue
4
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
DOI
10.1093/bioinformatics/btae171
PMC
PMC11018535
OpenAlex
W4393407391
Cited by
0
References
4
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
Locations
  • Bioinformatics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • UPCommons institutional repository (Universitat Politècnica de Catalunya) (submittedVersion, cc-by-nc-nd)
  • Dipòsit Digital de Documents de la UAB (Universitat Autònoma de Barcelona) (submittedVersion, cc-by)
Funders
  • La Caixa Junior Leader Fellowship (LCF/BQ/PI18/11630003)
  • Spanish Ministry of Science (RYC2019-026415-I, PID2019-107043RA-I00)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
protein structure, genetic variants, genomic data interpretation, command-line tool, genome annotation
MeSH terms
Proteins, Software, Biological Specimen Banks, Genomics

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