title: Protemot: prediction of protein binding sites with automatically extracted geometrical templates.
abstract: Geometrical analysis of protein tertiary substructures has been an effective approach employed to predict protein binding sites. This article presents the Protemot web server that carries out prediction of protein binding sites based on the structural templates automatically extracted from the crystal structures of protein-ligand complexes in the PDB (Protein Data Bank). The automatic extraction mechanism is essential for creating and maintaining a comprehensive template library that timely accommodates to the new release of PDB as the number of entries continues to grow rapidly. The design of Protemot is also distinctive by the mechanism employed to expedite the analysis process that matches the tertiary substructures on the contour of the query protein with the templates in the library. This expediting mechanism is essential for providing reasonable response time to the user as the number of entries in the template library continues to grow rapidly due to rapid growth of the number of entries in PDB. This article also reports the experiments conducted to evaluate the prediction power delivered by the Protemot web server. Experimental results show that Protemot can deliver a superior prediction power than a web server based on a manually curated template library with insufficient quantity of entries.
  
  
  BACKGROUND
  http://protemot.csie.ntu.edu.tw/step1.cgi http://bioinfo.mc.ntu.edu.tw/protemot/step1.cgi.
authors.affiliation: Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 106, Taiwan, Republic of China. darby@csie.ntu.edu.tw
authors.forename: Darby Tien-Hao
authors.initials: DT
authors.lastname: Chang
authors.forename: Yi-Zhong
authors.initials: YZ
authors.lastname: Weng
authors.forename: Jung-Hsin
authors.initials: JH
authors.lastname: Lin
authors.forename: Ming-Jing
authors.initials: MJ
authors.lastname: Hwang
authors.forename: Yen-Jen
authors.initials: YJ
authors.lastname: Oyang
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software; D040681:Structural Homology, Protein; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins