title: Critical assessment of structure-based sequence alignment methods at distant relationships.
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.
authors.affiliation: National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore 560065, India.
authors.forename: Singarevelu
authors.initials: S
authors.lastname: Kalaimathy
authors.forename: Ramanathan
authors.initials: R
authors.lastname: Sowdhamini
authors.forename: Karuppiah
authors.initials: K
authors.lastname: Kanagarajadurai
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods
chemical_list: D011506:Proteins