VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit Selection
Virtual screening of large chemical libraries is essential to support computer-aided drug development, providing a rapid and low-cost approach for further experimental validation. However, existing computational packages are often for specialised users or platform limited. Previously, we developed V...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2024-02-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/25/4/2002 |
| _version_ | 1797298069542273024 |
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| author | Rashid Hussain Andrew Scott Hackett Sandra Álvarez-Carretero Lydia Tabernero |
| author_facet | Rashid Hussain Andrew Scott Hackett Sandra Álvarez-Carretero Lydia Tabernero |
| author_sort | Rashid Hussain |
| collection | DOAJ |
| description | Virtual screening of large chemical libraries is essential to support computer-aided drug development, providing a rapid and low-cost approach for further experimental validation. However, existing computational packages are often for specialised users or platform limited. Previously, we developed VSpipe, an open-source semi-automated pipeline for structure-based virtual screening. We have now improved and expanded the initial command-line version into an interactive graphical user interface: VSpipe-GUI, a cross-platform open-source Python toolkit functional in various operating systems (e.g., Linux distributions, Windows, and Mac OS X). The new implementation is more user-friendly and accessible, and considerably faster than the previous version when AutoDock Vina is used for docking. Importantly, we have introduced a new compound selection module (i.e., spatial filtering) that allows filtering of docked compounds based on specified features at the target binding site. We have tested the new VSpipe-GUI on the Hepatitis C Virus NS3 (HCV NS3) protease as the target protein. The pocket-based and interaction-based modes of the spatial filtering module showed efficient and specific selection of ligands from the virtual screening that interact with the HCV NS3 catalytic serine 139. |
| first_indexed | 2024-03-07T22:29:31Z |
| format | Article |
| id | doaj.art-415b457f29034c99932e3f3858c9f081 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-07T22:29:31Z |
| publishDate | 2024-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-415b457f29034c99932e3f3858c9f0812024-02-23T15:19:21ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672024-02-01254200210.3390/ijms25042002VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit SelectionRashid Hussain0Andrew Scott Hackett1Sandra Álvarez-Carretero2Lydia Tabernero3School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UKSchool of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UKBristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TH, UKSchool of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PT, UKVirtual screening of large chemical libraries is essential to support computer-aided drug development, providing a rapid and low-cost approach for further experimental validation. However, existing computational packages are often for specialised users or platform limited. Previously, we developed VSpipe, an open-source semi-automated pipeline for structure-based virtual screening. We have now improved and expanded the initial command-line version into an interactive graphical user interface: VSpipe-GUI, a cross-platform open-source Python toolkit functional in various operating systems (e.g., Linux distributions, Windows, and Mac OS X). The new implementation is more user-friendly and accessible, and considerably faster than the previous version when AutoDock Vina is used for docking. Importantly, we have introduced a new compound selection module (i.e., spatial filtering) that allows filtering of docked compounds based on specified features at the target binding site. We have tested the new VSpipe-GUI on the Hepatitis C Virus NS3 (HCV NS3) protease as the target protein. The pocket-based and interaction-based modes of the spatial filtering module showed efficient and specific selection of ligands from the virtual screening that interact with the HCV NS3 catalytic serine 139.https://www.mdpi.com/1422-0067/25/4/2002virtual screeningchemoinformaticsVSpipeVSpipe-GUIAutoDockAutoDock Vina |
| spellingShingle | Rashid Hussain Andrew Scott Hackett Sandra Álvarez-Carretero Lydia Tabernero VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit Selection International Journal of Molecular Sciences virtual screening chemoinformatics VSpipe VSpipe-GUI AutoDock AutoDock Vina |
| title | VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit Selection |
| title_full | VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit Selection |
| title_fullStr | VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit Selection |
| title_full_unstemmed | VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit Selection |
| title_short | VSpipe-GUI, an Interactive Graphical User Interface for Virtual Screening and Hit Selection |
| title_sort | vspipe gui an interactive graphical user interface for virtual screening and hit selection |
| topic | virtual screening chemoinformatics VSpipe VSpipe-GUI AutoDock AutoDock Vina |
| url | https://www.mdpi.com/1422-0067/25/4/2002 |
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