title: A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction.
abstract: Protein sequence alignment is essential for template-based protein structure prediction and function annotation. We collect 20 sequence alignment algorithms, 10 published and 10 newly developed, which cover all representative sequence- and profile-based alignment approaches. These algorithms are benchmarked on 538 non-redundant proteins for protein fold-recognition on a uniform template library. Results demonstrate dominant advantage of profile-profile based methods, which generate models with average TM-score 26.5% higher than sequence-profile methods and 49.8% higher than sequence-sequence alignment methods. There is no obvious difference in results between methods with profiles generated from PSI-BLAST PSSM matrix and hidden Markov models. Accuracy of profile-profile alignments can be further improved by 9.6% or 21.4% when predicted or native structure features are incorporated. Nevertheless, TM-scores from profile-profile methods including experimental structural features are still 37.1% lower than that from TM-align, demonstrating that the fold-recognition problem cannot be solved solely by improving accuracy of structure feature predictions.
authors.affiliation: Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave, Ann Arbor, MI 48109.
authors.forename: Renxiang
authors.initials: R
authors.lastname: Yan
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.forename: Jianyi
authors.initials: J
authors.lastname: Yang
authors.forename: Sara
authors.initials: S
authors.lastname: Walker
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhang
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software
chemical_list: D011506:Proteins
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