DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis.
Saved in:
| Title: | DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis. |
|---|---|
| Authors: | Aureli, Simone, Marino, Daniele Di, Raniolo, Stefano, Limongelli, Vittorio |
| Source: | Bioinformatics; 12/15/2019, Vol. 35 Issue 24, p5328-5330, 3p |
| Subject Terms: | MOLECULAR dynamics, USER interfaces, MOLECULAR docking, INTERNET servers, PROTEIN binding, TRANCE protein |
| Abstract: | Motivation The ligand/protein binding interaction is typically investigated by docking and molecular dynamics (MD) simulations. In particular, docking-based virtual screening (VS) is used to select the best ligands from database of thousands of compounds, while MD calculations assess the energy stability of the ligand/protein binding complexes. Considering the broad use of these techniques, it is of great demand to have one single software that allows a combined and fast analysis of VS and MD results. With this in mind, we have developed the Drug Discovery Tool (DDT) that is an intuitive graphics user interface able to provide structural data and physico-chemical information on the ligand/protein interaction. Results DDT is designed as a plugin for the Visual Molecular Dynamics (VMD) software and is able to manage a large number of ligand/protein complexes obtained from AutoDock4 (AD4) docking calculations and MD simulations. DDT delivers four main outcomes: i) ligands ranking based on an energy score; ii) ligand ranking based on a ligands' conformation cluster analysis; iii) identification of the aminoacids forming the most occurrent interactions with the ligands; iv) plot of the ligands' center-of-mass coordinates in the Cartesian space. The flexibility of the software allows saving the best ligand/protein complexes using a number of user-defined options. Availability and implementation DDT_site_1 (alternative DDT_site_2); the DDT tutorial movie is available here. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR] |
| Copyright of Bioinformatics is the property of Oxford University Press / USA and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Complementary Index |
Full Text 
Full Text Finder 
Nájsť tento článok vo Web of Science Be the first to leave a comment!