ArticleBioinformatics (Oxford, England)2019
DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Enhanced Sampling and Tailored Collective Variables Yield Reproducible Free Energy Landscapes of Beta-1 Adrenergic Receptor Activation.Journal of chemical theory and computation · 2025Article
- Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study.Journal of chemical information and modeling · 2024Article
- Conformational plasticity and allosteric communication networks explain Shelterin protein TPP1 binding to human telomerase.Communications chemistry · 2023Article
- Subcellular location defines GPCR signal transduction.Science advances · 2023Article
- Phosphorylation of FAM134C by CK2 controls starvation-induced ER-phagy.Science advances · 2022Article
- Intelligent Evaluation of Public Sports Service Based on Intuitionistic Fuzzy Set Theory.Computational intelligence and neuroscience · 2022Article
- Drug Repurposing on G Protein-Coupled Receptors Using a Computational Profiling Approach.Frontiers in molecular biosciences · 2021Article
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4 authors.
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Abstract
motivationThe 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.
resultsDDT 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.
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