Adaptive BP-Dock: An Induced Fit Docking Approach for Full Receptor Flexibility

Ashini Bolia, Sefika Ozkan

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)734-746
Number of pages13
JournalJournal of Chemical Information and Modeling
Volume56
Issue number4
DOIs
StatePublished - Apr 25 2016

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Docks
flexibility
Conformations
fluctuation
drug
Ligands
Proteins
Scanning
Sampling
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Chemistry(all)
  • Chemical Engineering(all)
  • Computer Science Applications
  • Library and Information Sciences

Cite this

Adaptive BP-Dock : An Induced Fit Docking Approach for Full Receptor Flexibility. / Bolia, Ashini; Ozkan, Sefika.

In: Journal of Chemical Information and Modeling, Vol. 56, No. 4, 25.04.2016, p. 734-746.

Research output: Contribution to journalArticle

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