ArticleMolecules (Basel, Switzerland)2015
Reduction of false positives in structure-based virtual screening when receptor plasticity is considered.
Article in Molecules (Basel, Switzerland), 2015. 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, 32 citations in OpenAlex.
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- Machine intelligence-driven framework for optimized hit selection in virtual screening.Journal of cheminformatics · 2022Article
- Chemical system biology approach to identify multi-targeting FDA inhibitors for treating COVID-19 and associated health complications.Journal of biomolecular structure & dynamics · 2022Article
- Structure-Based Scaffold Repurposing toward the Discovery of Novel Cholinesterase Inhibitors.ACS omega · 2020Article
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- Structure-Based Virtual Screening: From Classical to Artificial Intelligence.Frontiers in chemistry · 2020Review
- Molecular Docking Studies of HIV-1 Resistance to Reverse Transcriptase Inhibitors: Mini-Review.Molecules (Basel, Switzerland) · 2018Review
- Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration.Scientific reports · 2017Article
- Evaluation of a novel virtual screening strategy using receptor decoy binding sites.Journal of negative results in biomedicine · 2016Article
- Exploring Flexibility of Progesterone Receptor Ligand Binding Domain Using Molecular Dynamics.PloS one · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structure-based virtual screening for selecting potential drug candidates is usually challenged by how numerous false positives in a molecule library are excluded when receptor plasticity is considered. In this study, based on the binding energy landscape theory, a hypothesis that a true inhibitor can bind to different conformations of the binding site favorably was put forth, and related strategies to defeat this challenge were devised; reducing false positives when receptor plasticity is considered. The receptor in the study is the influenza A nucleoprotein, whose oligomerization is a requirement for RNA binding. The structural flexibility of influenza A nucleoprotein was explored by molecular dynamics simulations. The resultant distinctive structures and the crystal structure were used as receptor models in docking exercises in which two binding sites, the tail-loop binding pocket and the RNA binding site, were targeted with the Otava PrimScreen1 diversity-molecule library using the GOLD software. The intersection ligands that were listed in the top-ranked molecules from all receptor models were selected. Such selection strategy successfully distinguished high-affinity and low-affinity control molecules added to the molecule library. This work provides an applicable approach for reducing false positives and selecting true ligands from molecule libraries.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.