title: Structure-based classification of FAD binding sites: A comparative study of structural alignment tools.
abstract: A total of six different structural alignment tools (TM-Align, TriangleMatch, CLICK, ProBis, SiteEngine and GA-SI) were assessed for their ability to perform two particular tasks: (i) discriminating FAD (flavin adenine dinucleotide) from non-FAD binding sites, and (ii) performing an all-to-all comparison on a set of 883 FAD binding sites for the purpose of classifying them. For the first task, the consistency of each alignment method was evaluated, showing that every method is able to distinguish FAD and non-FAD binding sites with a high Matthews correlation coefficient. Additionally, GA-SI was found to provide alignments different from those of the other approaches. The results obtained for the second task revealed more significant differences among alignment methods, as reflected in the poor correlation of their results and highlighted clearly by the independent evaluation of the structural superimpositions generated by each method. The classification itself was performed using the combined results of all methods, using the best result found for each comparison of binding sites. A number of different clustering methods (Single-linkage, UPGMA, Complete-linkage, SPICKER and k-Means clustering) were also used. The groups of similar binding sites (proteins) or clusters generated by the best performing method were further analyzed in terms of local sequence identity, local structural similarity and conservation of analogous contacts with the FAD ligands. Each of the clusters was characterized by a unique set of structural features or patterns, demonstrating that the groups generated truly reflect the structural diversity of FAD binding sites. Proteins 2016; 84:1728-1747. © 2016 Wiley Periodicals, Inc.
authors: Biocenter Oulu, and Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 University of Oulu, Oulu, Finland.
authors: Leonardo D
authors: LD
authors: Garma
authors: Department of Biochemistry and Molecular and Cellular Biology, Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Zaragoza, 50009, Spain.
authors: Milagros
authors: M
authors: Medina
authors: Biocenter Oulu, and Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 University of Oulu, Oulu, Finland. andre.juffer@oulu.fi.
authors: André H
authors: AH
authors: Juffer
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D016000:Cluster Analysis; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry*; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D012984:Software; D013329:Structure-Activity Relationship
chemical_list: D011506:Proteins; D005182:Flavin-Adenine Dinucleotide
keywords: FAD; binding site comparison; sequence independent; structural alignment; structural similarity