ArticleInternational journal of molecular sciences2020
A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0.
Article in International journal of molecular sciences, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Emerging two-dimensional nanomaterial and its modifications for enhanced antiviral applications: a review.Royal Society open science · 2025Review
- Computer aided design of inhibitor molecules against Vpr protein from different HIV-1 subtypes.In silico pharmacology · 2025Article
- A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2.ACS omega · 2023Article
- Progress of the "Molecular Informatics" Section in 2022.International journal of molecular sciences · 2023Article
- Identifying promising druggable binding sites and their flexibility to target the receptor-binding domain of SARS-CoV-2 spike protein.Computational and structural biotechnology journal · 2023Article
- Exscalate4CoV: Innovative High Performing Computing (HPC) Strategies to Tackle Pandemic Crisis.International journal of molecular sciences · 2022Article
- Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort.Scientific data · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Article
- Characterization of raloxifene as a potential pharmacological agent against SARS-CoV-2 and its variants.Cell death & disease · 2022Article
- Natural Compounds Inhibit SARS-CoV-2 nsp13 Unwinding and ATPase Enzyme Activities.ACS pharmacology & translational science · 2022Article
- Drug repositioning: A bibliometric analysis.Frontiers in pharmacology · 2022Review
- Scaffold Hybridization Strategy Leads to the Discovery of Dopamine DACS chemical neuroscience · 2021Article
- SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms.Molecular systems biology · 2021Article
- Blue Biotechnology: Computational Screening ofMarine drugs · 2021Article
- A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics.ACS pharmacology & translational science · 2021Article
- 2D MXenes with antiviral and immunomodulatory properties: A pilot study against SARS-CoV-2.Nano today · 2021Article
- A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization.Scientific reports · 2021Article
- The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.Briefings in bioinformatics · 2021Review
- A computational approach for the screening of potential antiviral compounds against SARS-CoV-2 protease: Ionic liquid vs herbal and natural compounds.Journal of molecular liquids · 2021Article
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Authors and funding
10 authors.
Funding
Abstract
(1) Background: Virtual screening studies on the therapeutically relevant proteins of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) require a detailed characterization of their druggable binding sites, and, more generally, a convenient pocket mapping represents a key step for structure-based in silico studies; (2) Methods: Along with a careful literature search on SARS-CoV-2 protein targets, the study presents a novel strategy for pocket mapping based on the combination of pocket (as performed by the well-known FPocket tool) and docking searches (as performed by PLANTS or AutoDock/Vina engines); such an approach is implemented by the Pockets 2.0 plug-in for the VEGA ZZ suite of programs; (3) Results: The literature analysis allowed the identification of 16 promising binding cavities within the SARS-CoV-2 proteins and the here proposed approach was able to recognize them showing performances clearly better than those reached by the sole pocket detection; and (4) Conclusions: Even though the presented strategy should require more extended validations, this proved successful in precisely characterizing a set of SARS-CoV-2 druggable binding pockets including both orthosteric and allosteric sites, which are clearly amenable for virtual screening campaigns and drug repurposing studies. All results generated by the study and the Pockets 2.0 plug-in are available for download.
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