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Assessing the Performance of Metadynamics and Path Variables in Predicting the Binding Free Energies of p38 Inhibitors

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Outgoing claims: the papers this work cites, builds on, or argues with.

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Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant
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Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors
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A Collective Variable for the Efficient Exploration of Protein Beta-Sheet Structures: Application to SH3 and GB1
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Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
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Flexible Docking in Solution Using Metadynamics
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Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics
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The Different Flexibility of c-Src and c-Abl Kinases Regulates the Accessibility of a Druggable Inactive Conformation
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Improved Scoring of Ligand−Protein Interactions Using OWFEG Free Energy Grids
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Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System
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Discovery of a Novel Binding Trench in HIV Integrase
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Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase
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Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring
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Signal integration by JNK and p38 MAPK pathways in cancer development
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Structural basis for p38α MAP kinase quinazolinone and pyridol-pyrimidine inhibitor specificity
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Mechanisms and functions of p38 MAPK signalling
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Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
inferredcites →https://doi.org/10.1093/protein/7.3.385openalex-snapshot
A new method for predicting binding affinity in computer-aided drug design
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Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches

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