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Pipeline for transferring annotations between proteins beyond globular domains.

Elizabeth Martínez-Pérez1,2, Mátyás Pajkos3, Silvio C E Tosatto4

  • 1Bioinformatics Unit, Fundación Instituto Leloir/IIBBA, Buenos Aires, Argentina.

Protein Science : a Publication of the Protein Society
|May 11, 2023
PubMed
Summary
This summary is machine-generated.

We developed a pipeline to transfer functional annotations between homologous intrinsically disordered proteins (IDPs). This method expands the knowledge of IDP functions across species, aiding biological role understanding.

Keywords:
DisProtannotationhomology transferintrinsically disordered proteinsmultiple sequence alignmentontology termsorthologous proteins

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Structural Biology

Background:

  • Intrinsically disordered proteins (IDPs) lack stable 3D structures and are crucial for various cellular processes.
  • DisProt is a manually curated database of experimentally verified IDPs, but its coverage is limited.
  • Transferring annotations to homologous proteins is vital for understanding IDP functions across species.

Purpose of the Study:

  • To evaluate the transferability of annotation terms from DisProt to orthologous proteins.
  • To develop a robust computational pipeline for transferring annotations of intrinsically disordered proteins.
  • To provide a web server (HoTIDP) for accessing these transferred annotations.

Main Methods:

  • Utilized DisProt as the source of experimentally verified IDP annotations.
  • Identified orthologs for DisProt entries and performed multiple sequence alignments (MSAs).
  • Implemented quality control for MSAs to ensure alignment accuracy before annotation transfer.

Main Results:

  • Successfully transferred 301,190 terms to 97,555 orthologous proteins from 1731 DisProt entries.
  • Developed a pipeline capable of generating high-quality MSAs for rapidly evolving disordered sequences.
  • Launched the HoTIDP web server (http://hotidp.leloir.org.ar) for public access to results and pipeline execution.

Conclusions:

  • Homology-based annotation transfer is feasible and highly scalable for intrinsically disordered proteins.
  • The HoTIDP server significantly expands the functional annotation landscape for IDPs.
  • This approach facilitates deeper insights into the biological roles of disordered proteins across diverse species.