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FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility

https://doi.org/10.1002/prot.25230
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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/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
inferredcites →https://doi.org/10.1002/prot.10393openalex-snapshot
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
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.21117openalex-snapshot
PIPER: An FFT‐based protein docking program with pairwise potentials
inferredcites →https://doi.org/10.1002/prot.22629openalex-snapshot
DynaDock: A new molecular dynamics‐based algorithm for protein–peptide docking including receptor flexibility
inferredcites →https://doi.org/10.1002/prot.22716openalex-snapshot
Sub-angstrom modeling of complexes between flexible peptides and globular proteins
inferredcites →https://doi.org/10.1002/prot.22818openalex-snapshot
Docking and scoring protein interactions: CAPRI 2009
inferredcites →https://doi.org/10.1002/prot.22921openalex-snapshot
Role of conformational sampling in computing mutation‐induced changes in protein structure and stability
inferredcites →https://doi.org/10.1002/prot.24356openalex-snapshot
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
inferredcites →https://doi.org/10.1002/prot.24422openalex-snapshot
Detection of peptide‐binding sites on protein surfaces: The first step toward the modeling and targeting of peptide‐mediated interactions
inferredcites →https://doi.org/10.1002/prot.24425openalex-snapshot
Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27
inferredcites →https://doi.org/10.1002/prot.24428openalex-snapshot
Docking, scoring, and affinity prediction in CAPRI
inferredcites →https://doi.org/10.1002/prot.24439openalex-snapshot
Blind prediction of interfacial water positions in CAPRI
inferredcites →https://doi.org/10.1002/prot.25064openalex-snapshot
Critical assessment of methods of protein structure prediction: Progress and new directions in round XI
inferredcites →https://doi.org/10.1002/prot.25215openalex-snapshot
Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition
inferredcites →https://doi.org/10.1006/jmbi.1994.1334openalex-snapshot
Satisfying Hydrogen Bonding Potential in Proteins
inferredcites →https://doi.org/10.1006/jmbi.2000.3642openalex-snapshot
Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-α11Edited by K. Nagai
inferredcites →https://doi.org/10.1007/978-1-4939-2285-7_10openalex-snapshot
Information-Driven Modeling of Protein-Peptide Complexes
inferredcites →https://doi.org/10.1016/0022-2836(92)90260-qopenalex-snapshot
Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution
inferredcites →https://doi.org/10.1016/bs.apcsb.2016.06.002openalex-snapshot
Recent Advances in Computational Models for the Study of Protein–Peptide Interactions
inferredcites →https://doi.org/10.1016/j.bbamcr.2010.10.012openalex-snapshot
The importin β binding domain as a master regulator of nucleocytoplasmic transport
inferredcites →https://doi.org/10.1016/j.biochi.2014.01.011openalex-snapshot
Molecular basis of the binding of YAP transcriptional regulator to the ErbB4 receptor tyrosine kinase
inferredcites →https://doi.org/10.1016/j.cbpa.2013.10.011openalex-snapshot
Druggable protein–protein interactions – from hot spots to hot segments
inferredcites →https://doi.org/10.1016/j.chembiol.2014.09.001openalex-snapshot
Small-Molecule Inhibitors of Protein-Protein Interactions: Progressing toward the Reality
inferredcites →https://doi.org/10.1016/j.jmb.2006.05.022openalex-snapshot
Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein−Protein Interface
inferredcites →https://doi.org/10.1016/j.jmb.2011.09.031openalex-snapshot
Community-Wide Assessment of Protein-Interface Modeling Suggests Improvements to Design Methodology
inferredcites →https://doi.org/10.1016/j.jmb.2012.05.015openalex-snapshot
Biophysical Basis of the Binding of WWOX Tumor Suppressor to WBP1 and WBP2 Adaptors
inferredcites →https://doi.org/10.1016/j.sbi.2013.07.006openalex-snapshot
Peptide docking and structure-based characterization of peptide binding: from knowledge to know-how
inferredcites →https://doi.org/10.1016/j.sbi.2016.05.017openalex-snapshot
Novel function discovery through sequence and structural data mining
inferredcites →https://doi.org/10.1016/j.str.2015.03.010openalex-snapshot
AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking
inferredcites →https://doi.org/10.1016/j.str.2015.05.021openalex-snapshot
Fully Blind Peptide-Protein Docking with pepATTRACT
inferredcites →https://doi.org/10.1016/j.str.2016.02.002openalex-snapshot
Structure-Based Identification of HDAC8 Non-histone Substrates
inferredcites →https://doi.org/10.1016/j.str.2016.07.021openalex-snapshot
Fully Blind Docking at the Atomic Level for Protein-Peptide Complex Structure Prediction
inferredcites →https://doi.org/10.1016/s0022-2836(02)00442-4openalex-snapshot
Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations
inferredcites →https://doi.org/10.1021/bi400987kopenalex-snapshot
Molecular Origin of the Binding of WWOX Tumor Suppressor to ErbB4 Receptor Tyrosine Kinase
inferredcites →https://doi.org/10.1038/314235a0openalex-snapshot
Hydrogen bonding and biological specificity analysed by protein engineering
inferredcites →https://doi.org/10.1038/77923openalex-snapshot
Structure of a WW domain containing fragment of dystrophin in complex with beta-dystroglycan.
inferredcites →https://doi.org/10.1038/emboj.2011.305openalex-snapshot
Structure of the SSB–DNA polymerase III interface and its role in DNA replication
inferredcites →https://doi.org/10.1038/nmeth0109-3openalex-snapshot
Predicting free energy changes using structural ensembles
inferredcites →https://doi.org/10.1038/nprot.2015.043openalex-snapshot
The FTMap family of web servers for determining and characterizing ligand-binding hot spots of proteins
inferredcites →https://doi.org/10.1073/pnas.0407280102openalex-snapshot
The modular architecture of protein–protein binding interfaces
inferredcites →https://doi.org/10.1073/pnas.1318001111openalex-snapshot
Structural mechanisms of PriA-mediated DNA replication restart
inferredcites →https://doi.org/10.1073/pnas.202485799openalex-snapshot
A simple physical model for binding energy hot spots in protein–protein complexes
inferredcites →https://doi.org/10.1073/pnas.97.19.10383openalex-snapshot
Native protein sequences are close to optimal for their structures
inferredcites →https://doi.org/10.1074/jbc.m113.527473openalex-snapshot
Structural and Biochemical Basis for Ubiquitin Ligase Recruitment by Arrestin-related Domain-containing Protein-3 (ARRDC3)
inferredcites →https://doi.org/10.1074/jbc.m115.651208openalex-snapshot
Crucial Roles of Single Residues in Binding Affinity, Specificity, and Promiscuity in the Cellulosomal Cohesin-Dockerin Interface
inferredcites →https://doi.org/10.1074/jbc.m115.655134openalex-snapshot
Interaction with Single-stranded DNA-binding Protein Stimulates Escherichia coli Ribonuclease HI Enzymatic Activity
inferredcites →https://doi.org/10.1074/jbc.m303275200openalex-snapshot
Structural Basis for the Specificity of Bipartite Nuclear Localization Sequence Binding by Importin-α
inferredcites →https://doi.org/10.1074/jbc.m307162200openalex-snapshot
Dissection of the Karyopherin α Nuclear Localization Signal (NLS)-binding Groove
inferredcites →https://doi.org/10.1074/jbc.m807017200openalex-snapshot
Six Classes of Nuclear Localization Signals Specific to Different Binding Grooves of Importin α
inferredcites →https://doi.org/10.1093/bioinformatics/btr254openalex-snapshot
A graphical interface for the FoldX forcefield
inferredcites →https://doi.org/10.1093/bioinformatics/btt691openalex-snapshot
mCSM: predicting the effects of mutations in proteins using graph-based signatures
inferredcites →https://doi.org/10.1093/bioinformatics/btu682openalex-snapshot
Comment on ‘protein–protein binding affinity prediction from amino acid sequence’
inferredcites →https://doi.org/10.1093/bioinformatics/btw133openalex-snapshot
PinaColada: peptide–inhibitor ant colony ad-hoc design algorithm
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gks398openalex-snapshot
PepSite: prediction of peptide-binding sites from protein surfaces
inferredcites →https://doi.org/10.1093/nar/gku404openalex-snapshot
PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces
inferredcites →https://doi.org/10.1093/nar/gkv1291openalex-snapshot
ELM 2016—data update and new functionality of the eukaryotic linear motif resource
inferredcites →https://doi.org/10.1093/nar/gkv456openalex-snapshot
CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site
inferredcites →https://doi.org/10.1093/nar/gkv495openalex-snapshot
GalaxyPepDock: a protein–peptide docking tool based on interaction similarity and energy optimization
inferredcites →https://doi.org/10.1093/protein/gzp030openalex-snapshot
Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details
inferredcites →https://doi.org/10.1093/protein/gzw020openalex-snapshot
Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes
inferredcites →https://doi.org/10.1111/tra.12098openalex-snapshot
Distinctive Conformation of Minor Site‐Specific Nuclear Localization Signals Bound to Importin‐α
inferredcites →https://doi.org/10.1126/science.7529940openalex-snapshot
A Hot Spot of Binding Energy in a Hormone-Receptor Interface
inferredcites →https://doi.org/10.1126/science.aad8865openalex-snapshot
De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity
inferredcites →https://doi.org/10.1371/journal.pcbi.1002170openalex-snapshot
Identification of a Novel Class of Farnesylation Targets by Structure-Based Modeling of Binding Specificity
inferredcites →https://doi.org/10.1371/journal.pone.0018934openalex-snapshot
Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors
inferredcites →https://doi.org/10.1371/journal.pone.0130433openalex-snapshot
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design
inferredcites →https://doi.org/10.1371/journal.pone.0161879openalex-snapshot
DockQ: A Quality Measure for Protein-Protein Docking Models
inferredcites →https://doi.org/10.2174/092986610791760342openalex-snapshot
Protein Core Adaptability: Crystal Structures of the Cavity-Filling Variants of Escherichia coli RNase HI
inferredcites →https://doi.org/10.2174/092986613804725208openalex-snapshot
metaPIS: A Sequence-based Meta-server for Protein Interaction Site Prediction
inferredcites →https://doi.org/10.7554/elife.00828openalex-snapshot
Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3

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.3313openalex-snapshot
Web‐accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE)
inferred← citeshttps://doi.org/10.1002/pro.3771openalex-snapshot
Flexible docking of peptides to proteins using CABS‐dock
inferred← citeshttps://doi.org/10.1002/pro.70338openalex-snapshot
DiffPepDock : Efficient protein–peptide docking and binder screening via SE (3)‐equivariant diffusion
inferred← citeshttps://doi.org/10.1002/prot.25871openalex-snapshot
Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45
inferred← citeshttps://doi.org/10.1002/prot.26313openalex-snapshot
Insights into protein–DNA interactions from hydrogen bond energy‐based comparative protein–ligand analyses
inferred← citeshttps://doi.org/10.1002/prot.26493openalex-snapshot
ComparePD : Improving protein– DNA complex model comparison with hydrogen bond energy‐based metrics
inferred← citeshttps://doi.org/10.1007/978-1-0716-0708-4_16openalex-snapshot
Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures
inferred← citeshttps://doi.org/10.1007/s10989-019-09985-2openalex-snapshot
Molecular Docking Analysis of 120 Potential HPV Therapeutic Epitopes Using a New Analytical Method
inferred← citeshttps://doi.org/10.1016/bs.mie.2024.04.013openalex-snapshot
Use of phosphotyrosine-containing peptides to target SH2 domains: Antagonist peptides of the Crk/CrkL-p130Cas axis
inferred← citeshttps://doi.org/10.1016/j.drudis.2018.05.006openalex-snapshot
Protein–peptide docking: opportunities and challenges
inferred← citeshttps://doi.org/10.1016/j.plrev.2017.07.003openalex-snapshot
Toward more efficient simulations of slow processes in large biomolecular systems
inferred← citeshttps://doi.org/10.1021/acs.jcim.1c00836openalex-snapshot
Predicting Protein–Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01084openalex-snapshot
PepPCBench is a Comprehensive Benchmarking Framework for Protein–Peptide Complex Structure Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01330openalex-snapshot
Thermodynamics of Disassembly and Denaturation of Protein Crystals in Osmolyte Solutions
inferred← citeshttps://doi.org/10.1021/acsomega.5c00967openalex-snapshot
Learning with Privileged Knowledge Distillation for Improved Peptide–Protein Docking
inferred← citeshttps://doi.org/10.1038/s41467-021-27838-9openalex-snapshot
Harnessing protein folding neural networks for peptide–protein docking
inferred← citeshttps://doi.org/10.1093/bib/bby080openalex-snapshot
Protein–peptide docking using CABS-dock and contact information
inferred← citeshttps://doi.org/10.1101/2024.09.03.609139openalex-snapshot
Evaluating Cross-linking-driven integrative modeling in peptide-HLAII complexes prediction with insights for refining predictive accuracy
inferred← citeshttps://doi.org/10.1101/2025.04.08.647699openalex-snapshot
PepPCBench is a Comprehensive Benchmark for Protein-Peptide Complex Structure Prediction with AlphaFold3
inferred← citeshttps://doi.org/10.1186/s12900-018-0083-6openalex-snapshot
re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1005905openalex-snapshot
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
inferred← citeshttps://doi.org/10.18502/ajmb.v15i1.11419openalex-snapshot
Opportunistic Challenges of Computer-aided Drug Discovery of Lipopeptides: New Insights for Large Molecule Therapeutics
inferred← citeshttps://doi.org/10.3389/fmolb.2021.669431openalex-snapshot
In silico Approaches for the Design and Optimization of Interfering Peptides Against Protein–Protein Interactions
inferred← citeshttps://doi.org/10.3390/antiox12030665openalex-snapshot
From In Silico to a Cellular Model: Molecular Docking Approach to Evaluate Antioxidant Bioactive Peptides
inferred← citeshttps://doi.org/10.35459/tbp.2019.000147openalex-snapshot
PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design
inferred← citeshttps://doi.org/10.53964/id.2024015openalex-snapshot
Covalent Flexible Peptide Docking in Drug Discovery: Current Challenges and Potential Interventions
inferred← citeshttps://doi.org/10.64898/2026.04.21.720042openalex-snapshot
Systematic Evaluation of AlphaFold2 and OpenFold3 on Protein–Peptide Complexes
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