VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization

Shun Liu; Jianchao Zhou; Ziyan Feng; Jiawen Zhang; Shuang Li; Zilong Jin; Chenfei Zhang; Shiliang Li; Gaoqi He; Honglin Li

doi:10.1093/bioinformatics/btac615

VRPharmer: bringing virtual reality into pharmacophore-based virtual screening with interactive exploration and realistic visualization

Bioinformatics. 2022 Oct 31;38(21):4953-4955. doi: 10.1093/bioinformatics/btac615.

Authors

Shun Liu¹, Jianchao Zhou², Ziyan Feng³, Jiawen Zhang¹, Shuang Li³, Zilong Jin¹, Chenfei Zhang¹, Shiliang Li³, Gaoqi He¹, Honglin Li^{1

3

4

5}

Affiliations

¹ School of Computer Science and Technology, East China Normal University, Shanghai 200062, China.
² Department of Computer Science and Engineering, East China University of Science and Technology, Shanghai 200237, China.
³ Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, Shanghai 200237, China.
⁴ Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai 200062, China.
⁵ Lingang Laboratory, Shanghai 200031, China.

PMID: 36073903
DOI: 10.1093/bioinformatics/btac615

Abstract

Summary: Current pharmacophore-based virtual screening (VS) software has limited interactive capabilities and less intuitive screening processes. In this study, a novel tool named VRPharmer is proposed to perform the entire VS workflow in VR environments. VRPharmer enables users to interactively perceive computation processes and immersively observe molecular structures. Besides a typical screening mode (OPT mode), VRPharmer provides a unique interactive screening mode (SCORE mode) for freely exploring the optimal binding poses. Pharmacophore models are editable to study the impact of each feature and further refine the screening results. Moreover, molecular rendering algorithms are improved for precise representations.

Availability and implementation: VRPharmer is open-source software under the MIT license. The released version is available at https://github.com/VRPharmer/VRPharmer.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Molecular Structure
Software*
Virtual Reality*
Workflow