ArticleMolecules (Basel, Switzerland)2016
AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking.
Article in Molecules (Basel, Switzerland), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 64 citations in OpenAlex.
- Rationally Designed Dual Kinase Inhibitors for Management of Obstructive Sleep Apnea-A Computational Study.Biomedicines · 2026Article
- Solvation Energetic Costs of Cognate Binding Site Formation.Journal of chemical information and modeling · 2025Article
- The Art and Science of Molecular Docking.Annual review of biochemistry · 2024Review
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- 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
- Inhibitory effects ofHeliyon · 2023Article
- Assessing How Residual Errors of Scoring Functions Correlate to Ligand Structural Features.International journal of molecular sciences · 2022Article
- Article
- Predicting Protein-Ligand Docking Structure with Graph Neural Network.Journal of chemical information and modeling · 2022Review
- CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function.Briefings in bioinformatics · 2022Article
- PlaceWaters: Real-time, explicit interface water sampling during Rosetta ligand docking.PloS one · 2022Article
- Computational healthcare: Present and future perspectives (Review).Experimental and therapeutic medicine · 2021Review
- AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings.Journal of chemical information and modeling · 2021Article
- Thermodynamic Decomposition of Solvation Free Energies with Particle Mesh Ewald and Long-Range Lennard-Jones Interactions in Grid Inhomogeneous Solvation Theory.Journal of chemical theory and computation · 2021Article
- An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.Journal of computer-aided molecular design · 2020Article
- Guiding Conventional Protein-Ligand Docking Software with Convolutional Neural Networks.Journal of chemical information and modeling · 2020Article
- Solvation Thermodynamics in Different Solvents: Water-Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory.Journal of chemical information and modeling · 2020Article
- An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.ChemRxiv : the preprint server for chemistry · 2020Article
- Applications of water molecules for analysis of macromolecule properties.Computational and structural biotechnology journal · 2020Review
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Water plays a significant role in the binding process between protein and ligand. However, the thermodynamics of water molecules are often underestimated, or even ignored, in protein-ligand docking. Usually, the free energies of active-site water molecules are substantially different from those of waters in the bulk region. The binding of a ligand to a protein causes a displacement of these waters from an active site to bulk, and this displacement process substantially contributes to the free energy change of protein-ligand binding. The free energy of active-site water molecules can be calculated by grid inhomogeneous solvation theory (GIST), using molecular dynamics (MD) and the trajectory of a target protein and water molecules. Here, we show a case study of the combination of GIST and a docking program and discuss the effectiveness of the displacing gain of unfavorable water in protein-ligand docking. We combined the GIST-based desolvation function with the scoring function of AutoDock4, which is called AutoDock-GIST. The proposed scoring function was assessed employing 51 ligands of coagulation factor Xa (FXa), and results showed that both scoring accuracy and docking success rate were improved. We also evaluated virtual screening performance of AutoDock-GIST using FXa ligands in the directory of useful decoys-enhanced (DUD-E), thus finding that the displacing gain of unfavorable water is effective for a successful docking campaign.
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