Abstract：
:In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and Recognition System). First, the most probable protonations, as defined by this rule based system, were compared to the ones stored in the well-known, manually revised CCDC/ASTEX data set. Then, to investigate the influence of the ligand protonation state on the docking results, different protonation states were created. Redocking and virtual screening experiments were conducted demonstrating that both docking programs have problems in identifying the correct protomer for each complex. Therefore, a preselection of plausible protomers or the improvement of the scoring functions concerning their ability to rank different molecules/states is needed. Additionally, ligand stereoisomers were tested for a subset of the CCDC/ASTEX set, showing similar problems regarding the ranking of these stereoisomers as the ranking of the protomers.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
ten Brink T,Exner TEdoi
10.1021/ci800420zsubject
Has Abstractpub_date
2009-06-01 00:00:00pages
1535-46issue
6eissn
1549-9596issn
1549-960Xjournal_volume
49pub_type
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更新日期：2007-03-01 00:00:00
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