Cargando…
VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform
Screening of ligand molecules to target proteins using computer-aided docking is a critical step in rational drug discovery. Based on this circumstance, we attempted to develop a virtual screening application system, named VSDK Virtual Screening by Docking, which can function under the Windows platf...
Autores principales: | , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Biomedical Informatics
2011
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3181425/ https://www.ncbi.nlm.nih.gov/pubmed/21976864 |
_version_ | 1782212756722679808 |
---|---|
author | Baba, Natsumi Akaho, Eiichi |
author_facet | Baba, Natsumi Akaho, Eiichi |
author_sort | Baba, Natsumi |
collection | PubMed |
description | Screening of ligand molecules to target proteins using computer-aided docking is a critical step in rational drug discovery. Based on this circumstance, we attempted to develop a virtual screening application system, named VSDK Virtual Screening by Docking, which can function under the Windows platform. This is a user-friendly, flexible, and versatile tool which can be used by users who are familiar with Windows OS. The virtual screening performance was tested for an arbitrarily-selected receptor, FGFR tyrosine kinase (pdb code: 1agw), by using ligands downloaded from ZINC database with its grid size of x,y,z = 30,30,30 and run number of 10. It took 90 minutes for 100 molecules for this virtual screening. VSDK is freely available at the designated URL, and a simplified manual can be downloaded from VSDK home page. This tool will have a more challenging scope and achievement as the computer speed and accuracy are increased and secured in the future. AVAILABILITY: The database is available for free at http://www.pharm.kobegakuin.ac.jp/˜akaho/english_top.html |
format | Online Article Text |
id | pubmed-3181425 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Biomedical Informatics |
record_format | MEDLINE/PubMed |
spelling | pubmed-31814252011-10-05 VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform Baba, Natsumi Akaho, Eiichi Bioinformation Software Screening of ligand molecules to target proteins using computer-aided docking is a critical step in rational drug discovery. Based on this circumstance, we attempted to develop a virtual screening application system, named VSDK Virtual Screening by Docking, which can function under the Windows platform. This is a user-friendly, flexible, and versatile tool which can be used by users who are familiar with Windows OS. The virtual screening performance was tested for an arbitrarily-selected receptor, FGFR tyrosine kinase (pdb code: 1agw), by using ligands downloaded from ZINC database with its grid size of x,y,z = 30,30,30 and run number of 10. It took 90 minutes for 100 molecules for this virtual screening. VSDK is freely available at the designated URL, and a simplified manual can be downloaded from VSDK home page. This tool will have a more challenging scope and achievement as the computer speed and accuracy are increased and secured in the future. AVAILABILITY: The database is available for free at http://www.pharm.kobegakuin.ac.jp/˜akaho/english_top.html Biomedical Informatics 2011-08-02 /pmc/articles/PMC3181425/ /pubmed/21976864 Text en © 2011 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited. |
spellingShingle | Software Baba, Natsumi Akaho, Eiichi VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform |
title | VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform |
title_full | VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform |
title_fullStr | VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform |
title_full_unstemmed | VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform |
title_short | VSDK: Virtual screening of small molecules using AutoDock Vina on Windows platform |
title_sort | vsdk: virtual screening of small molecules using autodock vina on windows platform |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3181425/ https://www.ncbi.nlm.nih.gov/pubmed/21976864 |
work_keys_str_mv | AT babanatsumi vsdkvirtualscreeningofsmallmoleculesusingautodockvinaonwindowsplatform AT akahoeiichi vsdkvirtualscreeningofsmallmoleculesusingautodockvinaonwindowsplatform |