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BP-Dock: A Flexible Docking Scheme for Exploring Protein–Ligand Interactions Based on Unbound Structures

https://doi.org/10.1021/ci4004927
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Flexible ligand docking to multiple receptor conformations: a practical alternative
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The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances
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Molecular Roots of Degenerate Specificity in Syntenin's PDZ2 Domain
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Protein flexibility in docking and surface mapping
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On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking
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GalaxyDock: Protein–Ligand Docking with Flexible Protein Side-chains
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Incorporating Backbone Flexibility in MedusaDock Improves Ligand-Binding Pose Prediction in the CSAR2011 Docking Benchmark
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Docking Ligands into Flexible and Solvated Macromolecules. 1. Development and Validation of FITTED 1.0
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Docking Ligands into Flexible and Solvated Macromolecules. 3. Impact of Input Ligand Conformation, Protein Flexibility, and Water Molecules on the Accuracy of Docking Programs
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Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange
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Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes
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Exploring Experimental Sources of Multiple Protein Conformations in Structure-Based Drug Design
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Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model
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Ligand−Protein DataBase: Linking Protein−Ligand Complex Structures to Binding Data
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Comparative Evaluation of 11 Scoring Functions for Molecular Docking
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Information Decay in Molecular Docking Screens against Holo, Apo, and Modeled Conformations of Enzymes
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Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
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Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance
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Exploiting Conformational Ensembles in Modeling Protein–Protein Interactions on the Proteome Scale
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A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility
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The Protein Data Bank
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RosettaBackrub--a web server for flexible backbone protein structure modeling and design
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Protein Structural Change Upon Ligand Binding: Linear Response Theory
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Use of an Induced Fit Receptor Structure in Virtual Screening
inferredcites →https://doi.org/10.1124/mol.57.3.474openalex-snapshot
A Single Glycine Residue at the Entrance to the First Membrane-Spanning Domain of the γ-Aminobutyric Acid Type A Receptor β2Subunit Affects Allosteric Sensitivity to GABA and Anesthetics
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A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family
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Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein
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Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning
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