ArticleInternational journal of molecular sciences2019
A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments.
Article in International journal of molecular sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
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- Data on molecular docking and molecular dynamics targetingData in brief · 2024Article
- Identification of Novel Antimicrobial Compounds TargetingMolecules (Basel, Switzerland) · 2024Article
- Applications of Machine Learning (ML) and Mathematical Modeling (MM) in Healthcare with Special Focus on Cancer Prognosis and Anticancer Therapy: Current Status and Challenges.Pharmaceutics · 2024Review
- Structural analysis, virtual screening and molecular simulation to identify potential inhibitors targeting 2'-O-ribose methyltransferase of SARS-CoV-2 coronavirus.Journal of biomolecular structure & dynamics · 2022Article
- Artificial intelligence to deep learning: machine intelligence approach for drug discovery.Molecular diversity · 2021Review
- Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace.Briefings in bioinformatics · 2021Review
- Isolation and Characterization of Compounds fromInternational journal of molecular sciences · 2021Article
- Prioritizing potential ACE2 inhibitors in the COVID-19 pandemic: Insights from a molecular mechanics-assisted structure-based virtual screening experiment.Journal of molecular graphics & modelling · 2020Article
- Structure-based drug repositioning over the human TMPRSS2 protease domain: search for chemical probes able to repress SARS-CoV-2 Spike protein cleavages.European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences · 2020Article
- Article
- Demystifying the Molecular Basis of Pyrazoloquinolinones Recognition at the Extracellular α1+/β3- Interface of the GABAFrontiers in pharmacology · 2020Article
- MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions.Expert opinion on drug discoveryArticle
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Authors and funding
9 authors.
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Abstract
Chemical biology and drug discovery are complex and costly processes. In silico screening approaches play a key role in the identification and optimization of original bioactive molecules and increase the performance of modern chemical biology and drug discovery endeavors. Here, we describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening (via the web service MTiOpenScreen), and molecular mechanics optimization (via the web service AMMOS2 [Automatic Molecular Mechanics Optimization for in silico Screening]). The online tools FAF-Drugs4, MTiOpenScreen, and AMMOS2 are implemented in the freely accessible RPBS (Ressource Parisienne en Bioinformatique Structurale) platform. The proposed protocol allows users to screen thousands of small molecules and to download the top 1500 docked molecules that can be further processed online. Users can then decide to purchase a small list of compounds for in vitro validation. To demonstrate the potential of this online-based protocol, we performed virtual screening experiments of 4574 approved drugs against three cancer targets. The results were analyzed in the light of published drugs that have already been repositioned on these targets. We show that our protocol is able to identify active drugs within the top-ranked compounds. The web-based protocol is user-friendly and can successfully guide the identification of new promising molecules for chemical biology and drug discovery purposes.
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