idTarget: a web server for identifying protein targets of small chemical molecules with robust scoring functions and a divide-and-conquer docking approach.
Identification of possible protein targets of small chemical molecules is an important step for unravelling their underlying causes of actions at the molecular level. To this end, we construct a web server, idTarget, which can predict possible binding targets of a small chemical molecule via a divide-and-conquer docking approach, in combination with our recently developed scoring functions based on robust regression analysis and quantum chemical charge models. Affinity profiles of the protein targets are used to provide the confidence levels of prediction. The divide-and-conquer docking approach uses adaptively constructed small overlapping grids to constrain the searching space, thereby achieving better docking efficiency. Unlike previous approaches that screen against a specific class of targets or a limited number of targets, idTarget screen against nearly all protein structures deposited in the Protein Data Bank (PDB). We show that idTarget is able to reproduce known off-targets of drugs or drug-like compounds, and the suggested new targets could be prioritized for further investigation. idTarget is freely available as a web-based server at http://idtarget.rcas.sinica.edu.tw.
Institute of Biomedical Engineering, National Taiwan University, Taipei, Taiwan.
Jui-Chih
JC
Wang
Pei-Ying
PY
Chu
Chung-Ming
CM
Chen
Jung-Hsin
JH
Lin
D000069454:Darunavir; D015195:Drug Design; D017320:HIV Protease Inhibitors / Q000737:chemistry; D056572:Histone Deacetylase Inhibitors / Q000737:chemistry; D007211:Indoles / Q000737:chemistry; D020407:Internet; D008024:Ligands; D008958:Models, Molecular; D010091:Oximes / Q000737:chemistry; D011487:Protein Conformation; D047428:Protein Kinase Inhibitors / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D012984:Software; D013449:Sulfonamides / Q000737:chemistry
C483321:6-bromoindirubin-3'-oxime; D017320:HIV Protease Inhibitors; D056572:Histone Deacetylase Inhibitors; D007211:Indoles; D008024:Ligands; D010091:Oximes; D047428:Protein Kinase Inhibitors; D011506:Proteins; D013449:Sulfonamides; D000069454:Darunavir