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Title:           Evaluating ligand docking methods for drugging protein–protein interfaces: insights from AlphaFold2 and molecular dynamics refinement
Subject:         Journal of Cheminformatics, https://doi.org/10.1186/s13321-025-01067-4
Keywords:        Protein interaction; Virtual screening; AlphaFold; Molecular docking; Molecular dynamics; Benchmarking
Author:          Jordi Gómez Borrego 
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     Item: 
      Title: Evaluating ligand docking methods for drugging protein–protein interfaces: insights from AlphaFold2 and molecular dynamics refinement
      Children: 
       Item: 
        Title:  
        Children: 
         Item: 
          Title: Abstract 
         Item: 
          Title: Scientific contribution 
       Item: 
        Title: Introduction
       Item: 
        Title: Results and discussion
        Children: 
         Item: 
          Title: AlphaFold2 models are suitable starting structures for molecular docking
         Item: 
          Title: Modeling truncated versus full-length proteins affects model quality
         Item: 
          Title: Conformational ensembles as starting structures for molecular docking
         Item: 
          Title: Evaluation of docking performance across strategies
         Item: 
          Title: Complementary metrics for docking effectiveness and binding pocket analysis
       Item: 
        Title: Conclusions
       Item: 
        Title: Methods
        Children: 
         Item: 
          Title: Compilation of PPI interactions with experimentally validated inhibitors
         Item: 
          Title: Protein structures and predictions
         Item: 
          Title: Modeling protein complexes
         Item: 
          Title: Comparison of models and native structures
         Item: 
          Title: Modeling protein conformational ensembles with AlphaFlow
         Item: 
          Title: Molecular dynamics simulations
         Item: 
          Title: Docking protocols
       Item: 
        Title: References
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