ArticleScientific reports2018
Water Pharmacophore: Designing Ligands using Molecular Dynamics Simulations with Water.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 37 citations in OpenAlex.
- Protein-Protein Interaction Stabilizers from MD Simulation-Derived Pharmacophores.Journal of chemical information and modeling · 2026Article
- Structure-Based Drug Discovery of Non-SAM-Mimetic Bisubstrate Inhibitors against NicotinamideACS medicinal chemistry letters · 2026Article
- Targeting epigenetic regulators: In-silico discovery of natural inhibitors against histone demethylase KDM4C.PloS one · 2026Article
- Water-Based Pharmacophore Modeling in Kinase Inhibitor Design: A Case Study on Fyn and Lyn Protein Kinases.Journal of chemical information and modeling · 2025Article
- Inductive-Associative Meta-learning Pipeline with Human Cognitive Patterns for Unseen Drug-Target Interaction Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Molecular Recognition and Modification Strategies of Umami Dipeptides with T1R1/T1R3 Receptors.Molecules (Basel, Switzerland) · 2025Article
- Transformation of peptides to small molecules in medicinal chemistry: Challenges and opportunities.Acta pharmaceutica Sinica. B · 2024Review
- Peptide-to-Small Molecule: Discovery of Non-Covalent, Active-Site Inhibitors of β-Herpesvirus Proteases.ACS medicinal chemistry letters · 2023Article
- The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering.International journal of molecular sciences · 2023Review
- WaterKit: Thermodynamic Profiling of Protein Hydration Sites.Journal of chemical theory and computation · 2023Article
- InhibitingPharmaceuticals (Basel, Switzerland) · 2023Article
- Computational Modelling and Sustainable Synthesis of a Highly Selective Electrochemical MIP-Based Sensor for Citalopram Detection.Molecules (Basel, Switzerland) · 2022Article
- An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.Journal of computer-aided molecular design · 2020Article
- An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.ChemRxiv : the preprint server for chemistry · 2020Article
- Fragment-based discovery of the first nonpeptidyl inhibitor of an S46 family peptidase.Scientific reports · 2019Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
In this study, we demonstrate a method to construct a water-based pharmacophore model which can be utilized in the absence of known ligands. This method utilizes waters found in the binding pocket, sampled through molecular dynamics. Screening of compound databases against this water-based pharmacophore model reveals that this approach can successfully identify known binders to a target protein. The method was tested by enrichment studies of 7 therapeutically important targets and compared favourably to screening-by-docking with Glide. Our results suggest that even without experimentally known binders, pharmacophore models can be generated using molecular dynamics with waters and used for virtual screening.
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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.