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ART‐RRT: As‐Rigid‐As‐Possible exploration of ligand unbinding pathways
Author(s) -
Nguyen Minh Khoa,
Jaillet Léonard,
Redon Stéphane
Publication year - 2018
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.25132
Subject(s) - morphing , computer science , computer graphics , dimensionality reduction , curse of dimensionality , graphics , state (computer science) , algorithm , theoretical computer science , mathematical optimization , artificial intelligence , mathematics , computer graphics (images)
This article proposes a method to efficiently generate approximate ligand unbinding pathways. It combines an efficient tree‐based exploration method with a morphing technique from Computer Graphics for dimensionality reduction. This method is computationally cheap and, unlike many existing approaches, does not require a reaction coordinate to guide the search. It can be used for finding pathways with known or unknown directions beforehand. The approach is evaluated on several benchmarks and the obtained solutions are compared with the results from other state‐of‐the‐art approaches. We show that the method is time‐efficient and produces pathways in good agreement with other state‐of‐the‐art solutions. These paths can serve as first approximations that can be used, analyzed, or improved with more specialized methods. © 2018 Wiley Periodicals, Inc.