ArticleJournal of computer-aided molecular design2019
Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison.
Article in Journal of computer-aided molecular design, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Machine Learning-Guided Repositioning of a SARS-CoV-2-Targeting Molecular Series as Cruzain Inhibitors.ChemMedChem · 2026Article
- WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families.JACS Au · 2025Article
- Exploring pocket-aware inhibitors of BTK kinase by generative deep learning, molecular docking, and molecular dynamics simulations.RSC advances · 2025Article
- Accelerated Hydration Site Localization and Thermodynamic Profiling.Journal of chemical information and modeling · 2025Article
- Effect of Water Networks On Ligand Binding: Computational Predictions vs Experiments.Journal of chemical information and modeling · 2024Article
- WatFinder: a ProDy tool for protein-water interactions.Bioinformatics (Oxford, England) · 2024Article
- The Three-Dimensional Reference Interaction Site Model Approach as a Promising Tool for Studying Hydrated Viruses and Their Complexes with Ligands.International journal of molecular sciences · 2024Review
- De novo prediction of explicit water molecule positions by a novel algorithm within the protein design software MUMBO.Scientific reports · 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
- In Silico Evaluation of the Thr58-Associated Conserved Water with KRAS Switch-II Pocket Binders.Journal of chemical information and modeling · 2023Article
- TWN-FS method: A novel fragment screening method for drug discovery.Computational and structural biotechnology journal · 2023Article
- Recent PELE Developments and Applications in Drug Discovery Campaigns.International journal of molecular sciences · 2022Review
- Ligand binding: evaluating the contribution of the water molecules network using the Fragment Molecular Orbital method.Journal of computer-aided molecular design · 2021Article
- Article
- Biotransformation: Impact and Application of Metabolism in Drug Discovery.ACS medicinal chemistry letters · 2020Article
- Article
- Efficient consideration of coordinated water molecules improves computational protein-protein and protein-ligand docking discrimination.PLoS computational biology · 2020Article
- Utilizing Grand Canonical Monte Carlo Methods in Drug Discovery.ACS medicinal chemistry letters · 2020Article
- A Molecular Dynamics Study of Vasoactive Intestinal Peptide Receptor 1 and the Basis of Its Therapeutic Antagonism.International journal of molecular sciences · 2019Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Targeting the interaction with or displacement of the 'right' water molecule can significantly increase inhibitor potency in structure-guided drug design. Multiple computational approaches exist to predict which waters should be targeted for displacement to achieve the largest gain in potency. However, the relative success of different methods remains underexplored. Here, we present a comparison of the ability of five water prediction programs (3D-RISM, SZMAP, WaterFLAP, WaterRank, and WaterMap) to predict crystallographic water locations, calculate their binding free energies, and to relate differences in these energies to observed changes in potency. The structural cohort included nine Bruton's Tyrosine Kinase (BTK) structures, and nine bromodomain structures. Each program accurately predicted the locations of most crystallographic water molecules. However, the predicted binding free energies correlated poorly with the observed changes in inhibitor potency when solvent atoms were displaced by chemical changes in closely related compounds.
Indexed as
Identifiers
30756207What OpenQuestion holds
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.