Critical assessment of structure-based sequence alignment methods at distant relationships

S. Kalaimathy, R. Sowdhamini, K. Kanagarajadurai
2011 Briefings in Bioinformatics  
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
more » ... eviation, 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.
doi:10.1093/bib/bbq025 pmid:21422071 fatcat:6bdx4dzvbreefjtr4w5r7ash3u