title: A study on the flexibility of enzyme active sites.
abstract: BACKGROUND
  A common assumption about enzyme active sites is that their structures are highly conserved to specifically distinguish between closely similar compounds. However, with the discovery of distinct enzymes with similar reaction chemistries, more and more studies discussing the structural flexibility of the active site have been conducted.
  
  
  RESULTS
  Most of the existing works on the flexibility of active sites focuses on a set of pre-selected active sites that were already known to be flexible. This study, on the other hand, proposes an analysis framework composed of a new data collecting strategy, a local structure alignment tool and several physicochemical measures derived from the alignments. The method proposed to identify flexible active sites is highly automated and robust so that more extensive studies will be feasible in the future. The experimental results show the proposed method is (a) consistent with previous works based on manually identified flexible active sites and (b) capable of identifying potentially new flexible active sites.
  
  
  CONCLUSIONS
  This proposed analysis framework and the former analyses on flexibility have their own advantages and disadvantage, depending on the cause of the flexibility. In this regard, this study proposes an alternative that complements previous studies and helps to construct a more comprehensive view of the flexibility of enzyme active sites.
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan. d95032@csie.ntu.edu.tw
authors.forename: Yi-Zhong
authors.initials: YZ
authors.lastname: Weng
authors.forename: Darby Tien-Hao
authors.initials: DT
authors.lastname: Chang
authors.forename: Yu-Feng
authors.initials: YF
authors.lastname: Huang
authors.forename: Chih-Wei
authors.initials: CW
authors.lastname: Lin
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods; D004798:Enzymes / Q000737:chemistry*; D011487:Protein Conformation; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D013329:Structure-Activity Relationship
chemical_list: D004798:Enzymes