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Updated: Jun 3, 2026

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
Published on: August 16, 2017
Critical assessment of structure-based sequence alignment methods at distant relationships
Singarevelu Kalaimathy1, Ramanathan Sowdhamini, Karuppiah Kanagarajadurai
1National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, India.
Abstract:
Accurate sequence alignments are crucial for modelling and to provide an evolutionary picture of related proteins. It is well-known that alignments are hard to obtain during distant relationships. Three thousand and fifty-two alignments of 218 pairs of protein domain structural entries, with <40% sequence identity, belonging to different structural classes, of diverse domain sizes and length-rigid/variable domains were performed using 12 programs. Structural parameters such as root mean square deviation, secondary-structural content and equivalences were considered for critical assessment. Methods that compare fragments and permit twists and translations align well during distant relationships and length variations.
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