IndelFR

IndelFR catalogs insertion and deletion (indel) events in protein structures and annotates their flanking regions to support analyses of indel impact on protein function and evolution.

Key Features:

• Extensive Data Collection: Contains 2,925,017 indels extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains across 1,053 SCOP superfamilies.
• Structural Alignment Basis: Identifies indels via pairwise alignments of homologous structures within SCOP superfamilies to reflect evolutionary relationships and structural variation.
• Flanking Region Annotation: Provides amino acid sequences, lengths, locations, secondary structure composition, hydrophilicity/hydrophobicity profiles, domain details, and 3D structure information for indel flanking regions.
• Evolutionary and Structural Context: Supplies data suitable for assessing the influence of indels on structural stability, functional diversity, and evolutionary trajectories.
• Non-redundant Domain Focus: Concentrates on known, non-redundant protein domains to support comparative and domain-level analyses.

Scientific Applications:

• Molecular Evolution Studies: Enables analysis of how indels contribute to protein evolution and divergence across SCOP superfamilies.
• Protein Engineering: Provides flanking-region sequence and structural data relevant to design and modification of proteins.
• Functional Impact and Disease Research: Facilitates investigation of functional consequences of indels and disease mechanisms linked to genetic variation.
• Comparative Structural Analysis: Supports comparative studies of homologous structures to examine structural variation and stability associated with indels.

Methodology:

IndelFR extracts indels from pairwise structural alignment pairs of non-redundant domains within SCOP superfamilies, focusing on known protein domains.