ArticlePloS one2017
Waterdock 2.0: Water placement prediction for Holo-structures with a pymol plugin.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Comparative Structure-Based Analysis of Predicted BZD9L1 Binding Modes Across Human Sirtuins.International journal of molecular sciences · 2026Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy.Journal of chemical information and modeling · 2025Article
- Accelerated Hydration Site Localization and Thermodynamic Profiling.Journal of chemical information and modeling · 2025Article
- Synergistic effect of antagonists to KRas4B/PDE6 molecular complex in pancreatic cancer.Life science alliance · 2023Article
- Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins.Nature communications · 2023Article
- WaterKit: Thermodynamic Profiling of Protein Hydration Sites.Journal of chemical theory and computation · 2023Article
- Water Networks in Complexes between Proteins and FDA-Approved Drugs.Journal of chemical information and modeling · 2023Article
- Boosting the Full Potential of PyMOL with Structural Biology Plugins.Biomolecules · 2022Review
- Imidazole and nitroimidazole derivatives as NADH-fumarate reductase inhibitors: Density functional theory studies, homology modeling, and molecular docking.Journal of computational chemistry · 2022Article
- Outliers in SAR and QSAR: 3. Importance of considering the role of water molecules in protein-ligand interactions and quantitative structure-activity relationship studies.Journal of computer-aided molecular design · 2021Article
- Accurate Prediction of Hydration Sites of Proteins Using Energy Model With Atom Embedding.Frontiers in molecular biosciences · 2021Article
- Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches.Molecules (Basel, Switzerland) · 2020Review
- PyVibMS: a PyMOL plugin for visualizing vibrations in molecules and solids.Journal of molecular modeling · 2020Article
- HomolWat: a web server tool to incorporate 'homologous' water molecules into GPCR structures.Nucleic acids research · 2020Article
- Applications of water molecules for analysis of macromolecule properties.Computational and structural biotechnology journal · 2020Review
- Incorporating Explicit Water Molecules and Ligand Conformation Stability in Machine-Learning Scoring Functions.Journal of chemical information and modeling · 2019Article
- Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins.The Journal of membrane biology · 2019Review
- Simulating Water Exchange to Buried Binding Sites.Journal of chemical theory and computation · 2019Article
- Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors.PloS one · 2019Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Water is often found to mediate interactions between a ligand and a protein. It can play a significant role in orientating the ligand within a binding pocket and contribute to the free energy of binding. It would thus be extremely useful to be able to accurately predict the position and orientation of water molecules within a binding pocket. Recently, we developed the WaterDock protocol that was able to predict 97% of the water molecules in a test set. However, this approach generated false positives at a rate of over 20% in most cases and whilst this might be acceptable for some applications, in high throughput scenarios this is not desirable. Here we tackle this problem via the inclusion of knowledge regarding the solvation structure of ligand functional groups. We call this new protocol WaterDock2 and demonstrate that this protocol maintains a similar true positive rate to the original implementation but is capable of reducing the false-positive rate by over 50%. To improve the usability of the method, we have also developed a plugin for the popular graphics program PyMOL. The plugin also contains an implementation of the original WaterDock.
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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.