Abstract：
:We present an induced fit docking approach called Adaptive BP-Dock that integrates perturbation response scanning (PRS) with the flexible docking protocol of RosettaLigand in an adaptive manner. We first perturb the binding pocket residues of a receptor and obtain a new conformation based on the residue response fluctuation profile using PRS. Next, we dock a ligand to this new conformation by RosettaLigand, where we repeat these steps for several iterations. We test this approach on several protein test sets including difficult unbound docking cases such as HIV-1 reverse transcriptase and HIV-1 protease. Adaptive BP-Dock results show better correlation with experimental binding affinities compared to other docking protocols. Overall, the results imply that Adaptive BP-Dock can easily capture binding induced conformational changes by simultaneous sampling of protein and ligand conformations. This can provide faster and efficient docking of novel targets for rational drug design.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Bolia A,Ozkan SBdoi
10.1021/acs.jcim.5b00587subject
Has Abstractpub_date
2016-04-25 00:00:00pages
734-46issue
4eissn
1549-9596issn
1549-960Xjournal_volume
56pub_type
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