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The ITS2 Database
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PASS2: update of database of structure-based sequence alignments.

Revathy Menon1, Soumya Nayak1, Rama Rajesh2

  • 1National Centre for Biological Sciences (Tata Institute of Fundamental Research), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India.

Database : the Journal of Biological Databases and Curation
|November 13, 2025
PubMed
Summary
This summary is machine-generated.

The Protein Alignment Organized as Structural Superfamilies (PASS2) database now includes structure-based sequence alignments for 26,690 protein domains. This update enhances evolutionary modeling and protein family recognition using the latest Structural Classification of Proteins extended (SCOPe) framework.

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Area of Science:

  • Structural biology
  • Bioinformatics
  • Computational biology

Background:

  • Protein sequence alignments are crucial for understanding protein evolution and function.
  • Aligning distantly related proteins is challenging due to low sequence identity.
  • Structural information can guide accurate alignments of divergent protein sequences.

Purpose of the Study:

  • To update and enhance the Protein Alignment Organized as Structural Superfamilies (PASS2) database.
  • To provide structure-based sequence alignments for protein domains within superfamilies.
  • To incorporate novel features for improved analysis of protein relationships and interactions.

Main Methods:

  • Utilized the Structural Classification of Proteins extended (SCOPe) framework (version 2.08).
  • Performed structure-guided sequence alignments for protein domains with <40% sequence identity.
  • Employed k-means clustering to partition divergent superfamilies and identified conserved interactions.

Main Results:

  • The PASS2.8 database contains alignments for 26,690 protein domains across 2058 superfamilies.
  • Included conserved secondary structural motifs, hidden Markov models (HMMs), and conserved residues.
  • Added topological diagrams, potential interactors, and updated conserved interaction methodologies.

Conclusions:

  • The updated PASS2 database provides valuable structure-based alignments and features for analyzing protein superfamilies.
  • Facilitates evolutionary studies, protein function prediction, and experimental design.
  • The new features offer deeper insights into protein domain relationships and interactions.