title: mFASD: a structure-based algorithm for discriminating different types of metal-binding sites.
abstract: BACKGROUND
  A large number of proteins contain metal ions that are essential for their stability and biological activity. Identifying and characterizing metal-binding sites through computational methods is necessary when experimental clues are lacking. Almost all published computational methods are designed to distinguish metal-binding sites from non-metal-binding sites. However, discrimination between different types of metal-binding sites is also needed to make more accurate predictions.
  
  
  RESULTS
  In this work, we proposed a novel algorithm called mFASD, which could discriminate different types of metal-binding sites effectively based on 3D structure data and is useful for accurate metal-binding site prediction. mFASD captures the characteristics of a metal-binding site by investigating the local chemical environment of a set of functional atoms that are considered to be in contact with the bound metal. Then a distance measure defined on functional atom sets enables the comparison between different metal-binding sites. The algorithm could discriminate most types of metal-binding sites from each other with high sensitivity and accuracy. We showed that cascading our method with existing ones could achieve a substantial improvement of the accuracy for metal-binding site prediction.
  
  
  METHODS
  Source code and data used are freely available from http://staff.ustc.edu.cn/∼liangzhi/mfasd/
authors: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
authors: Wei
authors: W
authors: He
authors: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
authors: Zhi
authors: Z
authors: Liang
authors: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
authors: Maikun
authors: M
authors: Teng
authors: Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China.
authors: Liwen
authors: L
authors: Niu
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D003198:Computer Simulation; D016002:Discriminant Analysis; D006801:Humans; D008670:Metals / Q000737:chemistry / Q000378:metabolism*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D008670:Metals; D011506:Proteins