PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe.

Pritha Ghosh,Oommen K Mathew,Teerna Bhattacharyya,Ramanathan Sowdhamini

doi:10.1093/database/baz028

Abstract

The number of protein structures is increasing due to the individual initiatives and rapid development of structure determination techniques. Structure-based sequence alignments of distantly related proteins enable the investigation of structural, evolutionary and functional relationships between proteins and their domains leading to their common evolutionary origin. Protein Alignments organized as Structural Superfamilies (PASS2) is a database that provides such alignments of members of protein domain superfamilies of known structure and with less than 40% sequence identity. PASS2 has been continuously updated in accordance to Structural Classification of Proteins (SCOP), and now Structural Classification of Proteins - extended (SCOPe). The current update directly corresponds to SCOPe 2.06, dealing with 2006 domain superfamilies of known structure and about 14 000 domains. Alignments have been augmented by features such as hidden Markov models, highly conserved residues, structural motifs and gene ontology terms, which are available for download. In this update, we introduce the concepts of ‘extreme structural outliers’ and ‘split superfamilies’ as well.

Highlights

With the rapid growth of structure determination methods, the number of protein structures deposited in the ProteinData Bank (PDB) has been growing exponentially
Homologous proteins are related by sequence, structure and function
Since structure is better conserved in evolution than sequence, structurebased sequence alignments have been commonly used as the gold standard for sequence alignment evaluation

Summary

Introduction

Data Bank (PDB) has been growing exponentially. This provides us with rich data to understand more about the protein structure–function relationships. It is important to classify the structures according to their. Vol 2019, Article ID baz evolutionary origin. For proteins of known structure, the Structural Classification of Proteins (SCOP) database provides comprehensive description of the structural and evolutionary relationships. And superfamily levels denote the close and distant evolutionary relationships between structural domains, respectively. SCOPe extends SCOP through a combination of automation and manual curation [1]

Methods

Results

Conclusion