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Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45

https://doi.org/10.1002/prot.25871
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What this work says

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

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Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
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A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds
inferredcites →https://doi.org/10.1002/pro.3320openalex-snapshot
PixelDB: Protein–peptide complexes annotated with structural conservation of the peptide binding mode
inferredcites →https://doi.org/10.1002/pro.3431openalex-snapshot
PixelDB: Protein–peptide complexes annotated with structural conservation of the peptide binding mode
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.22710openalex-snapshot
On the use of structural templates for high‐resolution docking
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.24428openalex-snapshot
Docking, scoring, and affinity prediction in 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.25230openalex-snapshot
FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility
inferredcites →https://doi.org/10.1002/prot.25788openalex-snapshot
NMR‐assisted protein structure prediction with MELDxMD
inferredcites →https://doi.org/10.1006/jmbi.1993.1626openalex-snapshot
Comparative Protein Modelling by Satisfaction of Spatial Restraints
inferredcites →https://doi.org/10.1006/jmbi.1997.0959openalex-snapshot
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions
inferredcites →https://doi.org/10.1007/978-1-4939-6798-8openalex-snapshot
Modeling Peptide-Protein Interactions
inferredcites →https://doi.org/10.1007/978-1-4939-6798-8_4openalex-snapshot
Template-Based Prediction of Protein-Peptide Interactions by Using GalaxyPepDock
inferredcites →https://doi.org/10.1007/978-1-4939-7000-1_26openalex-snapshot
Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive
inferredcites →https://doi.org/10.1007/978-1-61779-588-6_17openalex-snapshot
Modeling Peptide–Protein Interactions
inferredcites →https://doi.org/10.1016/j.febslet.2013.01.002openalex-snapshot
The tandem β‐zipper: Modular binding of tandem domains and linear motifs
inferredcites →https://doi.org/10.1016/j.jmb.2010.11.008openalex-snapshot
Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping
inferredcites →https://doi.org/10.1016/j.jmb.2018.02.015openalex-snapshot
Fuzziness in Protein Interactions—A Historical Perspective
inferredcites →https://doi.org/10.1016/j.sbi.2018.09.009openalex-snapshot
Affinity and specificity of motif-based protein–protein interactions
inferredcites →https://doi.org/10.1016/j.str.2009.11.012openalex-snapshot
The Structural Basis of Peptide-Protein Binding Strategies
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/10.1021/acs.jctc.6b00977openalex-snapshot
Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics
inferredcites →https://doi.org/10.1021/acs.jctc.6b00978openalex-snapshot
Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX
inferredcites →https://doi.org/10.1021/acs.jctc.7b00125openalex-snapshot
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design
inferredcites →https://doi.org/10.1021/acs.jctc.8b00886openalex-snapshot
MELD × MD Folds Nonthreadables, Giving Native Structures and Populations
inferredcites →https://doi.org/10.1021/acs.jctc.8b01208openalex-snapshot
Predicting Protein Dimer Structures Using MELD × MD
inferredcites →https://doi.org/10.1021/acs.jpcb.7b11367openalex-snapshot
Flex ddG: Rosetta Ensemble-Based Estimation of Changes in Protein–Protein Binding Affinity upon Mutation
inferredcites →https://doi.org/10.1021/bi500574zopenalex-snapshot
DYNLL2 Dynein Light Chain Binds to an Extended Linear Motif of Myosin 5a Tail That Has Structural Plasticity
inferredcites →https://doi.org/10.1038/nature06526openalex-snapshot
Reaching for high-hanging fruit in drug discovery at protein–protein interfaces
inferredcites →https://doi.org/10.1038/nprot.2016.169openalex-snapshot
The ClusPro web server for protein–protein docking
inferredcites →https://doi.org/10.1073/pnas.052706099openalex-snapshot
Natural β-sheet proteins use negative design to avoid edge-to-edge aggregation
inferredcites →https://doi.org/10.1073/pnas.1200678109openalex-snapshot
Templates are available to model nearly all complexes of structurally characterized proteins
inferredcites →https://doi.org/10.1073/pnas.1506788112openalex-snapshot
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference
inferredcites →https://doi.org/10.1073/pnas.1515561112openalex-snapshot
Accelerating molecular simulations of proteins using Bayesian inference on weak information
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.m113.459149openalex-snapshot
Structural Analysis of the Regulation of the DYNLL/LC8 Binding to Nek9 by Phosphorylation
inferredcites →https://doi.org/10.1093/bioinformatics/btx216openalex-snapshot
ClusPro PeptiDock: efficient global docking of peptide recognition motifs using FFT
inferredcites →https://doi.org/10.1093/bioinformatics/btx486openalex-snapshot
MFIB: a repository of protein complexes with mutual folding induced by binding
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1093/nar/gkl893openalex-snapshot
DisProt: the Database of Disordered Proteins
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/nar/gkz848openalex-snapshot
PhaSePro: the database of proteins driving liquid–liquid phase separation
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/10.1126/sciadv.1601274openalex-snapshot
Blind protein structure prediction using accelerated free-energy simulations
inferredcites →https://doi.org/10.1126/stke.2192004pl2openalex-snapshot
Computational Alanine Scanning of Protein-Protein Interfaces
inferredcites →https://doi.org/10.1371/journal.pcbi.1003926openalex-snapshot
ECOD: An Evolutionary Classification of Protein Domains
inferredcites →https://doi.org/10.1371/journal.pcbi.1005485openalex-snapshot
Modeling disordered protein interactions from biophysical principles
inferredcites →https://doi.org/10.1371/journal.pcbi.1005905openalex-snapshot
High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock
inferredcites →https://doi.org/10.1371/journal.pone.0002524openalex-snapshot
Contextual Specificity in Peptide-Mediated Protein Interactions
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.0023294openalex-snapshot
Generalized Fragment Picking in Rosetta: Design, Protocols and Applications
inferredcites →https://doi.org/10.1371/journal.pone.0058769openalex-snapshot
A Unified Conformational Selection and Induced Fit Approach to Protein-Peptide Docking

What points at this work

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

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Benchmarking of structure refinement methods for protein complex models
inferred← citeshttps://doi.org/10.1002/wcms.1470openalex-snapshot
Structural prediction of protein interactions and docking using conservation and coevolution
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DFT calculations of electronic structure evaluation and intermolecular interactions of p53-derived peptides with cytotoxic effect on breast cancer
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Evaluating GPCR modeling and docking strategies in the era of deep learning-based protein structure prediction
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Structural evolution of Delta lineage of SARS-CoV-2
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A combined in silico approach to design peptide ligands with increased receptor-subtype selectivity
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Computational structure modeling for diverse categories of macromolecular interactions
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MELD in Action: Harnessing Data to Accelerate Molecular Dynamics
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PAK4 phosphorylates and inhibits AMPKα to control glucose uptake
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Matching protein surface structural patches for high-resolution blind peptide docking
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Short linear motif based interactions and dynamics of the ezrin, radixin, moesin and merlin FERM domains
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Protein storytelling through physics
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Molecular Modelling in Bioactive Peptide Discovery and Characterisation
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Artificial Intelligence-Driven Discovery and Optimization of Antimicrobial Peptides Targeting ESKAPE Pathogens and Multidrug-Resistant Fungi
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Exploration and structural modelling of protein interactions using evolutionary information
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