ArticleCommunications chemistry2020
Elucidating the multiple roles of hydration for accurate protein-ligand binding prediction via deep learning.
Article in Communications chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Protein Science Meets Artificial Intelligence: A Systematic Review and a Biochemical Meta-Analysis of an Inter-Field.Frontiers in bioengineering and biotechnology · 2022Pooled it
- Peering inside the black box by learning the relevance of many-body functions in neural network potentials.Nature communications · 2025Article
- Modeling Molecularly Imprinted Nanoparticles with LNKD: A Resource Efficient Algorithm for Polymer Cross-Linking.Journal of chemical information and modeling · 2025Article
- AI-driven protein pocket detection through integrating deep Q-networks for structural analysis.Journal of computer-aided molecular design · 2025Article
- Investigating whether deep learning models for co-folding learn the physics of protein-ligand interactions.Nature communications · 2025Article
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- Cyclic peptide inhibitors function as molecular glues to stabilize Gq/11 heterotrimers.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Instruction multi-constraint molecular generation using a teacher-student large language model.BMC biology · 2025Article
- Repurposing major metabolites of lamiaceae family as potential inhibitors ofFrontiers in pharmacology · 2025Article
- Machine Learning in Enhancing Protein Binding Sites Predictions - What Has Changed Since Then?Combinatorial chemistry & high throughput screening · 2025Review
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- Absolute Binding Free Energies with OneOPES.The journal of physical chemistry letters · 2024Article
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- Comparative in silico analysis of CNS-active molecules targeting the blood-brain barrier choline transporter for Alzheimer's disease therapy.In silico pharmacology · 2024Article
- OneOPES, a Combined Enhanced Sampling Method to Rule Them All.Journal of chemical theory and computation · 2023Article
- The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering.International journal of molecular sciences · 2023Review
- Adaptive insertion of a hydrophobic anchor into a poly(ethylene glycol) host for programmable surface functionalization.Nature chemistry · 2023Article
- Deep generative molecular design reshapes drug discovery.Cell reports. Medicine · 2022Review
- Hydrogen bonding penalty used for virtual screening to discover potent inhibitors for Papain-Like cysteine proteases of SARS-CoV-2.Chemical biology & drug design · 2022Article
- Water regulates the residence time of Benzamidine in Trypsin.Nature communications · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate and efficient prediction of protein-ligand interactions has been a long-lasting dream of practitioners in drug discovery. The insufficient treatment of hydration is widely recognized to be a major limitation for accurate protein-ligand scoring. Using an integration of molecular dynamics simulations on thousands of protein structures with novel big-data analytics based on convolutional neural networks and deep Taylor decomposition, we consistently identify here three different patterns of hydration to be essential for protein-ligand interactions. In addition to desolvation and water-mediated interactions, the formation of enthalpically favorable networks of first-shell water molecules around solvent-exposed ligand moieties is identified to be essential for protein-ligand binding. Despite being currently neglected in drug discovery, this hydration phenomenon could lead to new avenues in optimizing the free energy of ligand binding. Application of deep neural networks incorporating hydration to docking provides 89% accuracy in binding pose ranking, an essential step for rational structure-based drug design.
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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.