Related Experiment Video
Updated: Jan 28, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with
Pritha Ghosh1, Teerna Bhattacharyya1, Oommen K Mathew1
1National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore, Karnataka, India.
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.
More Related Videos
07:38Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames
Published on: April 11, 2019
16:02Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
Published on: February 10, 2023
Related Concept Videos
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
Protein Families
Protein and Protein Structure
A protein's shape is critical to its function. For example, an enzyme...
Conservation of Protein Domains
The Scope of Physics
Structural Protein Function
Collagen, the most abundant protein in mammals, is found throughout the body. In connective tissue, such as skin, ligaments, and tendons, it provides tensile strength and elasticity. In bones and teeth, it mineralizes to...