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Integrating atom‐based and residue‐based scoring functions for protein–protein docking

https://doi.org/10.1002/pro.687
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What this work says

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

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ZDOCK predictions for the CAPRI challenge
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ZDOCK: An initial‐stage protein‐docking algorithm
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Combination of scoring functions improves discrimination in protein–protein docking
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Protein–protein docking benchmark 2.0: An update
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Optimal design of protein docking potentials: Efficiency and limitations
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ZRANK: Reranking protein docking predictions with an optimized energy function
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Integrating statistical pair potentials into protein complex prediction
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The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI
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A combination of rescoring and refinement significantly improves protein docking performance
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Protein–protein docking benchmark version 3.0
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Principles of flexible protein–protein docking
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Combining interface core and whole interface descriptors in postscan processing of protein‐protein docking models
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Performance of ZDOCK and ZRANK in CAPRI rounds 13–19
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Molecular Surface Complementarity at Protein-Protein Interfaces: The Critical Role Played by Surface Normals at Well Placed, Sparse, Points in Docking
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Determination of atomic desolvation energies from the structures of crystallized proteins
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Numerical recipes in C++: The art of scientific computing
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Accounting for conformational changes during protein–protein docking
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TOUCHSTONE II: A New Approach to Ab Initio Protein Structure Prediction
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Development of Unified Statistical Potentials Describing Protein-Protein Interactions
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Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
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HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
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Simulation of activation free energies in molecular systems
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Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
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A systematic study of low-resolution recognition in protein–protein complexes
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ClusPro: an automated docking and discrimination method for the prediction of protein complexes
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Accelerating and focusing protein–protein docking correlations using multi-dimensional rotational FFT generating functions
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D ockground protein–protein docking decoy set
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The RosettaDock server for local protein-protein docking
inferredcites →https://doi.org/10.1093/protein/14.2.105openalex-snapshot
Protein docking using continuum electrostatics and geometric fit
inferredcites →https://doi.org/10.1093/protein/8.4.371openalex-snapshot
Protein docking for low-resolution structures
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Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
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What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Benchmarking AlphaFold for protein complex modeling reveals accuracy determinants
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Performance of ZDOCK in CAPRI rounds 20–26
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Native fold and docking pose discrimination by the same residue‐based scoring function
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