ArticleJournal of cheminformatics2017
Systematic exploration of multiple drug binding sites.
Article in Journal of cheminformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
- Beyond the flat screen: evaluating virtual reality as a complementary tool for molecular docking in drug discovery.Journal of computer-aided molecular design · 2026Review
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- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
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- Lipid raft disruption inhibits the activation of Transient Receptor Potential Vanilloid 1, but not TRP Melastatin 3 and the voltage-gated L-type calcium channels in sensory neurons.Frontiers in cell and developmental biology · 2024Article
- Construction of Histone-Protein Complex Structures by Peptide Growing.International journal of molecular sciences · 2023Article
- The Cholesterol-Modulating Effect of the New Herbal Medicinal Recipe from Yellow Vine (Plants (Basel, Switzerland) · 2022Article
- Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design.International journal of molecular sciences · 2022Article
- Exploration of Somatostatin Binding Mechanism to Somatostatin Receptor Subtype 4.International journal of molecular sciences · 2022Article
- Unveiling the Possible Oryzalin-Binding Site in the α-Tubulin ofACS omega · 2022Article
- Prerequisite Binding Modes Determine the Dynamics of Action of Covalent Agonists of Ion Channel TRPA1.Pharmaceuticals (Basel, Switzerland) · 2021Article
- Determination of Ligand Binding Modes in Hydrated Viral Ion Channels to Foster Drug Design and Repositioning.Journal of chemical information and modeling · 2021Article
- Finding Druggable Sites in Proteins Using TACTICS.Journal of chemical information and modeling · 2021Article
- Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome.International journal of molecular sciences · 2020Review
- Towards Unraveling the Histone Code by Fragment Blind Docking.International journal of molecular sciences · 2019Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundTargets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple binding sites is often challenging. Blind docking has been widely used for fast mapping of the entire target surface for multiple binding sites. Reliability of blind docking is limited by approximations of hydration models, simplified handling of molecular flexibility, and imperfect search algorithms.
resultsTo overcome such limitations, the present study introduces Wrap 'n' Shake (WnS), an atomic resolution method that systematically "wraps" the entire target into a monolayer of ligand molecules. Functional binding sites are extracted by a rapid molecular dynamics shaker. WnS is tested on biologically important systems such as mitogen-activated protein, tyrosine-protein kinases, key players of cellular signaling, and farnesyl pyrophosphate synthase, a target of antitumor agents.
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Registered trials
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.