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How different from random are docking predictions when ranked by scoring functions?

https://doi.org/10.1002/prot.22844
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What this work says

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

inferredcites →https://doi.org/10.1002/(sici)1097-0134(19990515)35:3<364::aid-prot11>3.0.co;2-4openalex-snapshot
Use of pair potentials across protein interfaces in screening predicted docked complexes
inferredcites →https://doi.org/10.1002/prot.10383openalex-snapshot
ICM‐DISCO docking by global energy optimization with fully flexible side‐chains
inferredcites →https://doi.org/10.1002/prot.10384openalex-snapshot
Protein–protein docking predictions for the CAPRI experiment
inferredcites →https://doi.org/10.1002/prot.10389openalex-snapshot
ZDOCK: An initial‐stage protein‐docking algorithm
inferredcites →https://doi.org/10.1002/prot.10390openalex-snapshot
A protein–protein docking benchmark
inferredcites →https://doi.org/10.1002/prot.10394openalex-snapshot
Successful discrimination of protein interactions
inferredcites →https://doi.org/10.1002/prot.10395openalex-snapshot
Finding needles in haystacks: Reranking DOT results by using shape complementarity, cluster analysis, and biological information
inferredcites →https://doi.org/10.1002/prot.10460openalex-snapshot
RDOCK: Refinement of rigid‐body protein docking predictions
inferredcites →https://doi.org/10.1002/prot.20554openalex-snapshot
Classification of protein complexes based on docking difficulty
inferredcites →https://doi.org/10.1002/prot.20560openalex-snapshot
Protein–protein docking benchmark 2.0: An update
inferredcites →https://doi.org/10.1002/prot.21117openalex-snapshot
PIPER: An FFT‐based protein docking program with pairwise potentials
inferredcites →https://doi.org/10.1002/prot.21373openalex-snapshot
ZRANK: Reranking protein docking predictions with an optimized energy function
inferredcites →https://doi.org/10.1002/prot.21419openalex-snapshot
pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking
inferredcites →https://doi.org/10.1002/prot.21442openalex-snapshot
Identification of near‐native structures by clustering protein docking conformations
inferredcites →https://doi.org/10.1002/prot.21502openalex-snapshot
Integrating statistical pair potentials into protein complex prediction
inferredcites →https://doi.org/10.1002/prot.21698openalex-snapshot
Implicit flexibility in protein docking: Cross‐docking and local refinement
inferredcites →https://doi.org/10.1002/prot.21747openalex-snapshot
The performance of ZDOCK and ZRANK in rounds 6–11 of CAPRI
inferredcites →https://doi.org/10.1002/prot.21796openalex-snapshot
Prediction and scoring of docking poses with pyDock
inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot
Docking and scoring protein complexes: CAPRI 3rd Edition
inferredcites →https://doi.org/10.1002/prot.21920openalex-snapshot
A combination of rescoring and refinement significantly improves protein docking performance
inferredcites →https://doi.org/10.1002/prot.22106openalex-snapshot
Protein–protein docking benchmark version 3.0
inferredcites →https://doi.org/10.1006/jmbi.1997.1203openalex-snapshot
Modelling protein docking using shape complementarity, electrostatics and biochemical information 1 1Edited by J. Thornton
inferredcites →https://doi.org/10.1016/j.sbi.2009.02.008openalex-snapshot
Convergence and combination of methods in protein–protein docking
inferredcites →https://doi.org/10.1016/s0022-2836(03)00670-3openalex-snapshot
Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
inferredcites →https://doi.org/10.1016/s0959-440x(02)00285-3openalex-snapshot
Prediction of protein–protein interactions by docking methods
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1073/pnas.0802496105openalex-snapshot
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein–protein docking
inferredcites →https://doi.org/10.1073/pnas.75.1.303openalex-snapshot
Macromolecular shape and surface maps by solvent exclusion.
inferredcites →https://doi.org/10.1073/pnas.89.6.2195openalex-snapshot
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
inferredcites →https://doi.org/10.1093/bioinformatics/btg371openalex-snapshot
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
inferredcites →https://doi.org/10.1093/nar/gkh354openalex-snapshot
ClusPro: a fully automated algorithm for 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/10.1109/iembs.2004.1403850openalex-snapshot
Clustering protein-protein docking predictions
inferredcites →https://doi.org/10.1371/journal.pcbi.1000191openalex-snapshot
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
inferredcites →https://doi.org/10.1529/biophysj.104.058768openalex-snapshot
Optimal Clustering for Detecting Near-Native Conformations in Protein Docking

What points at this work

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

inferred← citeshttps://doi.org/10.1002/pro.585openalex-snapshot
On the analysis of protein–protein interactions via knowledge‐based potentials for the prediction of protein–protein docking
inferred← citeshttps://doi.org/10.1002/prot.24144openalex-snapshot
Characterizing the morphology of protein binding patches
inferred← citeshttps://doi.org/10.1007/978-3-319-07953-0_2openalex-snapshot
A Greedy Algorithm for Hierarchical Complete Linkage Clustering
inferred← citeshttps://doi.org/10.1016/b978-0-12-800168-4.00004-4openalex-snapshot
On the Use of Knowledge-Based Potentials for the Evaluation of Models of Protein–Protein, Protein–DNA, and Protein–RNA Interactions
inferred← citeshttps://doi.org/10.1016/j.jmb.2013.01.014openalex-snapshot
Understanding Protein–Protein Interactions Using Local Structural Features
inferred← citeshttps://doi.org/10.1016/j.sbi.2013.07.005openalex-snapshot
Towards a detailed atlas of protein–protein interactions
inferred← citeshttps://doi.org/10.1016/j.str.2011.10.023openalex-snapshot
Computational Reconstruction of Multidomain Proteins Using Atomic Force Microscopy Data
inferred← citeshttps://doi.org/10.1016/j.ymeth.2012.12.004openalex-snapshot
Advances in integrative modeling of biomolecular complexes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btt121openalex-snapshot
Specificity and affinity quantification of protein–protein interactions
inferred← citeshttps://doi.org/10.1093/bioinformatics/btx616openalex-snapshot
On the mechanisms of protein interactions: predicting their affinity from unbound tertiary structures
inferred← citeshttps://doi.org/10.1093/glycob/cws147openalex-snapshot
Solvent structure improves docking prediction in lectin–carbohydrate complexes
inferred← citeshttps://doi.org/10.1093/nar/gkr317openalex-snapshot
PRUNE and PROBE--two modular web services for protein-protein docking
inferred← citeshttps://doi.org/10.1098/rsif.2012.0835openalex-snapshot
On the binding affinity of macromolecular interactions: daring to ask why proteins interact
inferred← citeshttps://doi.org/10.1111/cbdd.13446openalex-snapshot
Suitability of MMGBSA for the selection of correct ligand binding modes from docking results
inferred← citeshttps://doi.org/10.1134/s1990750825600499openalex-snapshot
In Silico Determination, Engineering Demonstration, and Preliminary Docking Studies of Potential Antimicrobial Peptides from Cocosin-1 against Methicillin-Resistant Staphylococcus aureus (MRSA) Muramyl E (MurE) Ligase
inferred← citeshttps://doi.org/10.1371/journal.pone.0032647openalex-snapshot
On Docking, Scoring and Assessing Protein-DNA Complexes in a Rigid-Body Framework
inferred← citeshttps://doi.org/10.21203/rs.3.rs-2950957/v1openalex-snapshot
Revolutionizing Therapeutics: Synthesizing Substituted Biphenyls and Assessing Their Antimicrobial Properties, ADMET Properties, and Biofilm Inhibition Potential
inferred← citeshttps://doi.org/10.5772/37856openalex-snapshot
Structural Bioinformatics of Proteins: Predicting the Tertiary and Quaternary Structure of Proteins from Sequence
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