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Challenges and opportunities of automated protein‐protein docking: HDOCK server vs human predictions in CAPRI Rounds 38‐46

https://doi.org/10.1002/prot.25874
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What this work says

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

inferredcites →https://doi.org/10.1002/0471140864.ps0209s50openalex-snapshot
Comparative Protein Structure Modeling Using MODELLER
inferredcites →https://doi.org/10.1002/cpps.20openalex-snapshot
Comparative Protein Structure Modeling Using MODELLER
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An iterative knowledge‐based scoring function to predict protein–ligand interactions: I. Derivation of interaction potentials
inferredcites →https://doi.org/10.1002/jcc.20505openalex-snapshot
An iterative knowledge‐based scoring function to predict protein–ligand interactions: II. Validation of the scoring function
inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
inferredcites →https://doi.org/10.1002/prot.20264openalex-snapshot
Scoring function for automated assessment of protein structure template quality
inferredcites →https://doi.org/10.1002/prot.20551openalex-snapshot
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
inferredcites →https://doi.org/10.1002/prot.21214openalex-snapshot
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
inferredcites →https://doi.org/10.1002/prot.21612openalex-snapshot
Loop modeling: Sampling, filtering, and scoring
inferredcites →https://doi.org/10.1002/prot.21723openalex-snapshot
HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot
Docking and scoring protein complexes: CAPRI 3rd Edition
inferredcites →https://doi.org/10.1002/prot.21949openalex-snapshot
An iterative knowledge‐based scoring function for protein–protein recognition
inferredcites →https://doi.org/10.1002/prot.22797openalex-snapshot
MDockPP: A hierarchical approach for protein‐protein docking and its application to CAPRI rounds 15–19
inferredcites →https://doi.org/10.1002/prot.22850openalex-snapshot
Blind predictions of protein interfaces by docking calculations in CAPRI
inferredcites →https://doi.org/10.1002/prot.24343openalex-snapshot
Sampling and scoring: A marriage made in heaven
inferredcites →https://doi.org/10.1002/prot.24392openalex-snapshot
Global and local structural similarity in protein–protein complexes: Implications for template‐based docking
inferredcites →https://doi.org/10.1002/prot.24428openalex-snapshot
Docking, scoring, and affinity prediction in CAPRI
inferredcites →https://doi.org/10.1002/prot.24435openalex-snapshot
Inclusion of the orientational entropic effect and low‐resolution experimental information for protein–protein docking in Critical Assessment of PRedicted Interactions (CAPRI)
inferredcites →https://doi.org/10.1002/prot.25215openalex-snapshot
Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition
inferredcites →https://doi.org/10.1002/prot.25234openalex-snapshot
Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking
inferredcites →https://doi.org/10.1002/prot.25419openalex-snapshot
The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment
inferredcites →https://doi.org/10.1002/prot.25838openalex-snapshot
Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
inferredcites →https://doi.org/10.1002/prot.25870openalex-snapshot
Modeling protein‐protein, protein‐peptide, and protein‐oligosaccharide complexes: CAPRI 7th edition
inferredcites →https://doi.org/10.1006/jmbi.1999.3091openalex-snapshot
Protein secondary structure prediction based on position-specific scoring matrices 1 1Edited by G. Von Heijne
inferredcites →https://doi.org/10.1007/s41048-019-0088-0openalex-snapshot
CHDOCK: a hierarchical docking approach for modeling Cn symmetric homo-oligomeric complexes
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Computer analysis of protein-protein interaction
inferredcites →https://doi.org/10.1016/j.bpj.2014.08.033openalex-snapshot
Protein-Protein Docking: From Interaction to Interactome
inferredcites →https://doi.org/10.1016/j.bpj.2014.12.015openalex-snapshot
A Web Interface for Easy Flexible Protein-Protein Docking with ATTRACT
inferredcites →https://doi.org/10.1016/j.drudis.2014.02.005openalex-snapshot
Search strategies and evaluation in protein–protein docking: principles, advances and challenges
inferredcites →https://doi.org/10.1016/j.immuni.2017.12.008openalex-snapshot
Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12Rβ1
inferredcites →https://doi.org/10.1016/j.jmb.2003.07.006openalex-snapshot
The Relationship Between Sequence and Interaction Divergence in Proteins
inferredcites →https://doi.org/10.1016/j.sbi.2013.11.005openalex-snapshot
Template-based structure modeling of protein–protein interactions
inferredcites →https://doi.org/10.1021/acs.jcim.8b00142openalex-snapshot
Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides
inferredcites →https://doi.org/10.1038/msb.2011.75openalex-snapshot
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
inferredcites →https://doi.org/10.1038/nature11503openalex-snapshot
Structure-based prediction of protein–protein interactions on a genome-wide scale
inferredcites →https://doi.org/10.1038/nmeth.1818openalex-snapshot
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
inferredcites →https://doi.org/10.1038/nmeth.3213openalex-snapshot
The I-TASSER Suite: protein structure and function prediction
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.189openalex-snapshot
Helicobacter pylori adhesin HopQ engages in a virulence-enhancing interaction with human CEACAMs
inferredcites →https://doi.org/10.1038/nprot.2010.32openalex-snapshot
The HADDOCK web server for data-driven biomolecular docking
inferredcites →https://doi.org/10.1038/nprot.2010.5openalex-snapshot
I-TASSER: a unified platform for automated protein structure and function prediction
inferredcites →https://doi.org/10.1038/nprot.2016.169openalex-snapshot
The ClusPro web server for protein–protein docking
inferredcites →https://doi.org/10.1038/s41467-017-02784-7openalex-snapshot
Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space
inferredcites →https://doi.org/10.1073/pnas.092147999openalex-snapshot
Interrogating protein interaction networks through structural biology
inferredcites →https://doi.org/10.1073/pnas.102179699openalex-snapshot
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
inferredcites →https://doi.org/10.1093/bib/bbw027openalex-snapshot
Template-based protein–protein docking exploiting pairwise interfacial residue restraints
inferredcites →https://doi.org/10.1093/bioinformatics/btm404openalex-snapshot
Clustal W and Clustal X version 2.0
inferredcites →https://doi.org/10.1093/bioinformatics/btn093openalex-snapshot
3D-Garden: a system for modelling protein–protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
inferredcites →https://doi.org/10.1093/bioinformatics/btt038openalex-snapshot
SwarmDock: a server for flexible protein–protein docking
inferredcites →https://doi.org/10.1093/bioinformatics/btu097openalex-snapshot
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
inferredcites →https://doi.org/10.1093/emboj/cdf417openalex-snapshot
Structure of the periplasmic domain of Pseudomonas aeruginosa TolA: evidence for an evolutionary relationship with the TonB transporter protein
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gkh354openalex-snapshot
ClusPro: a fully automated algorithm for protein-protein docking
inferredcites →https://doi.org/10.1093/nar/gki481openalex-snapshot
PatchDock and SymmDock: servers for rigid and symmetric docking
inferredcites →https://doi.org/10.1093/nar/gki524openalex-snapshot
TM-align: a protein structure alignment algorithm based on the TM-score
inferredcites →https://doi.org/10.1093/nar/gkl206openalex-snapshot
GRAMM-X public web server for protein-protein docking
inferredcites →https://doi.org/10.1093/nar/gkn216openalex-snapshot
The RosettaDock server for local protein-protein docking
inferredcites →https://doi.org/10.1093/nar/gkq311openalex-snapshot
HexServer: an FFT-based protein docking server powered by graphics processors
inferredcites →https://doi.org/10.1093/nar/gkv368openalex-snapshot
pyDockSAXS: protein–protein complex structure by SAXS and computational docking
inferredcites →https://doi.org/10.1093/nar/gkw340openalex-snapshot
InterEvDock: a docking server to predict the structure of protein–protein interactions using evolutionary information
inferredcites →https://doi.org/10.1093/nar/gkx407openalex-snapshot
HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy
inferredcites →https://doi.org/10.1093/nar/gky1033openalex-snapshot
PubChem 2019 update: improved access to chemical data
inferredcites →https://doi.org/10.1093/nar/gky357openalex-snapshot
HPEPDOCK: a web server for blind peptide–protein docking based on a hierarchical algorithm
inferredcites →https://doi.org/10.1093/nar/gky398openalex-snapshot
HSYMDOCK: a docking web server for predicting the structure of protein homo-oligomers with Cn or Dn symmetry
inferredcites →https://doi.org/10.1110/ps.062501507openalex-snapshot
Efficient molecular docking of NMR structures: Application to HIV‐1 protease
inferredcites →https://doi.org/10.1111/jnc.14598openalex-snapshot
High‐affinity heterotetramer formation between the large myelin‐associated glycoprotein and the dynein light chain DYNLL 1
inferredcites →https://doi.org/10.1186/1758-2946-3-33openalex-snapshot
Open Babel: An open chemical toolbox
inferredcites →https://doi.org/10.1186/s12859-019-3270-yopenalex-snapshot
Pushing the accuracy limit of shape complementarity for protein-protein docking
inferredcites →https://doi.org/10.1186/s13321-017-0246-7openalex-snapshot
Efficient conformational ensemble generation of protein-bound peptides
inferredcites →https://doi.org/10.15252/embj.201798665openalex-snapshot
Helicobacter pylori adhesin HopQ disrupts trans dimerization in human CEACAMs
inferredcites →https://doi.org/10.2210/pdb6gbg/pdbopenalex-snapshot
Helicobacter pyloriadhesin HopQ disruptstransdimerization in human CEACAMs.
inferredcites →https://doi.org/10.5287/ora-wx6d7brkeopenalex-snapshot
Structure and mode of action of the TolA-TolB complex from Pseudomonas aeruginosa
inferredcites →https://doi.org/10.7554/elife.45222openalex-snapshot
Structural mechanisms of phospholipid activation of the human TPC2 channel

What points at this work

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

inferred← citeshttps://doi.org/10.1002/prot.26823openalex-snapshot
Protein Complex Structure Prediction With AlphaFold ‐Enhanced HDOCK in CAPRI Rounds 47–55
inferred← citeshttps://doi.org/10.1007/s10930-021-10031-8openalex-snapshot
Protein–Protein Docking: Past, Present, and Future
inferred← citeshttps://doi.org/10.1016/j.compbiolchem.2021.107620openalex-snapshot
In silico analysis and characterization of medicinal mushroom cystathionine beta-synthase as an angiotensin converting enzyme (ACE) inhibitory protein
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Probing the formation, structure and free energy relationships of M protein dimers of SARS-CoV-2
inferred← citeshttps://doi.org/10.1016/j.ecoenv.2025.119037openalex-snapshot
Carcinogenic risks of aromatic amines and their radical oxidation products: Construction of adverse outcome pathways, development of priority control lists, and mechanistic analysis of carcinogenesis
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2025.148692openalex-snapshot
DTL promotes pancreatic cancer progression through ubiquitin-mediated degradation of SMAD4
inferred← citeshttps://doi.org/10.1016/j.jhazmat.2023.131541openalex-snapshot
Innovative screening for functional improved aromatic amine derivatives: Toxicokinetics, free radical oxidation pathway and carcinogenic adverse outcome pathway
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01029openalex-snapshot
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01399openalex-snapshot
Revisiting Protein–Protein Docking: A Systematic Evaluation Framework
inferred← citeshttps://doi.org/10.1038/s41596-020-0312-xopenalex-snapshot
The HDOCK server for integrated protein–protein docking
inferred← citeshttps://doi.org/10.1088/1674-1056/abc14eopenalex-snapshot
Protein–protein docking with interface residue restraints*
inferred← citeshttps://doi.org/10.1101/2021.02.22.432196openalex-snapshot
Protein-protein docking with large-scale backbone flexibility using coarse-grained Monte-Carlo simulations
inferred← citeshttps://doi.org/10.2174/1568026620666201207095626openalex-snapshot
Docking Paradigm in Drug Design
inferred← citeshttps://doi.org/10.3390/ijms22147341openalex-snapshot
Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations
inferred← citeshttps://doi.org/10.5772/intechopen.106583openalex-snapshot
Molecular Docking in the Study of Ligand-Protein Recognition: An Overview
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