ArticleJournal of chemical theory and computation2010
Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
37 citing papers in PubMed, 83 citations in OpenAlex.
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- Leveraging a Separation of States Method for Relative Binding Free Energy Calculations in Systems with Trapped Waters.Journal of chemical theory and computation · 2024Article
- WaterKit: Thermodynamic Profiling of Protein Hydration Sites.Journal of chemical theory and computation · 2023Article
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- Incorporating structural similarity into a scoring function to enhance the prediction of binding affinities.Journal of cheminformatics · 2021Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- MovableType Software for Fast Free Energy-Based Virtual Screening: Protocol Development, Deployment, Validation, and Assessment.Journal of chemical information and modeling · 2020Article
- GemSpot: A Pipeline for Robust Modeling of Ligands into Cryo-EM Maps.Structure (London, England : 1993) · 2020Article
- Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach.The journal of physical chemistry. B · 2019Article
- The role of hydration effects in 5-fluorouridine binding to SOD1: insight from a new 3D-RISM-KH based protocol for including structural water in docking simulations.Journal of computer-aided molecular design · 2019Article
- Assessing and improving the performance of consensus docking strategies using the DockBox package.Journal of computer-aided molecular design · 2019Article
- Using AMBER18 for Relative Free Energy Calculations.Journal of chemical information and modeling · 2019Article
- Hydrogen-Bond-Dependent Conformational Switching: A Computational Challenge from Experimental Thermochemistry.The Journal of organic chemistry · 2019Article
- Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors.PloS one · 2019Article
- Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3.Journal of computer-aided molecular design · 2019Article
- Comparison of free-energy methods using a tripeptide-water model system.Journal of computational chemistry · 2018Article
- Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Monte Carlo free energy perturbation (MC/FEP) calculations have been applied to compute the relative binding affinities of 17 congeneric pyridazo-pyrimidinone inhibitors of the protein p38α MAP kinase. Overall correlation with experiment was found to be modest when the complexes were hydrated using a traditional procedure with a stored solvent box. Significant improvements in accuracy were obtained when the MC/FEP calculations were repeated using initial solvent distributions optimized by the water placement algorithm JAWS. The results underscore the importance of accurate placement of water molecules in a ligand binding site for the reliable prediction of relative free energies of binding.
Identifiers
What 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.