Protemot: prediction of protein binding sites with automatically extracted geometrical templates.
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.
Chang
Darby Tien-Hao
DT
Department of Computer Science and Information Engineering, National Taiwan University, Taipei, 106, Taiwan, Republic of China. darby@csie.ntu.edu.tw
Weng
Yi-Zhong
YZ
Lin
Jung-Hsin
JH
Hwang
Ming-Jing
MJ
Oyang
Yen-Jen
YJ
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
D008024:Ligands; D011506:Proteins