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HADDOCK2P2I: A Biophysical Model for Predicting the Binding Affinity of Protein–Protein Interaction Inhibitors

https://doi.org/10.1021/ci4005332
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What this work says

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

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Relationship between the inhibition constant (KI) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction
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Identification of Protein–Protein Interaction Sites from Docking Energy Landscapes
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The Thermodynamics of Protein–Ligand Interaction and Solvation: Insights for Ligand Design
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Molecular Interaction Fields and 3D-QSAR Studies of p53−MDM2 Inhibitors Suggest Additional Features of Ligand−Target Interaction
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Hot Spots and Transient Pockets: Predicting the Determinants of Small-Molecule Binding to a Protein–Protein Interface
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HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
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Fragment-Based Discovery of Bromodomain Inhibitors Part 2: Optimization of Phenylisoxazole Sulfonamides
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New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model
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Are Scoring Functions in Protein−Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark
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The HADDOCK web server for data-driven biomolecular docking
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BCL-2 family antagonists for cancer therapy
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Protein–protein interaction inhibitors get into the groove
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Molecular dynamics with coupling to an external bath
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Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure
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2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions
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PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure
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Flexibility and binding affinity in protein–ligand, protein–protein and multi-component protein interactions: limitations of current computational approaches
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On the binding affinity of macromolecular interactions: daring to ask why proteins interact
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PRODRG: a tool for high-throughput crystallography of protein–ligand complexes
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Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
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The Genetic Landscape of a Cell
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A Computer Program for Classifying Plants
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Structure of Bcl-x L -Bak Peptide Complex: Recognition Between Regulators of Apoptosis
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Calculation of Protein-Ligand Binding Affinities
inferredcites →https://doi.org/10.1186/1756-0500-5-367openalex-snapshot
ACPYPE - AnteChamber PYthon Parser interfacE
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Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods
inferredcites →https://doi.org/10.1371/journal.pone.0009598openalex-snapshot
Atomic Analysis of Protein-Protein Interfaces with Known Inhibitors: The 2P2I Database
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A Leap into the Chemical Space of Protein-Protein Interaction Inhibitors
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Computational Identification of Inhibitors of Protein-Protein Interactions

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