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Protein–protein docking predictions for the CAPRI experiment

https://doi.org/10.1002/prot.10384
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Effective energy function for proteins in solution
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Distantly related sequences in the alpha‐ and beta‐subunits of ATP synthase, myosin, kinases and other ATP‐requiring enzymes and a common nucleotide binding fold.
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Bayesian statistical analysis of protein side‐chain rotamer preferences
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Modeling of protein interactions in genomes
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An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families
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An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes
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Morphology of protein–protein interfaces
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Three-Dimensional Structure of the Complex between a T Cell Receptor β Chain and the Superantigen Staphylococcal Enterotoxin B
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A simple physical model for binding energy hot spots in protein–protein complexes
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Native protein sequences are close to optimal for their structures
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R: A Language for Data Analysis and Graphics
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X‐ray structure of HPr kinase: a bacterial protein kinase with a P‐loop nucleotide‐binding domain
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Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion
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MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison
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THE STRUCTURE AND FUNCTION OF THE HEMAGGLUTININ MEMBRANE GLYCOPROTEIN OF INFLUENZA VIRUS
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THE STRUCTURAL BASIS OF T CELL ACTIVATION BY SUPERANTIGENS

What points at this work

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

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De NovoStructure Prediction: Methods and Applications
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Protein–protein docking dealing with the unknown
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CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock
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Progress in protein–protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side‐chain flexibility
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Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition
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A simple reference state makes a significant improvement in near‐native selections from structurally refined docking decoys
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Antibodies as a model system for comparative model refinement
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A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13–19
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How different from random are docking predictions when ranked by scoring functions?
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In silico modeling of pH‐optimum of protein–protein binding
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Monte Carlo replica-exchange based ensemble docking of protein conformations
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Docking With Rosetta and Deep Learning Approaches in CAPRI Rounds 47–55
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Self-Association of Arrestin Family Members
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New Compstatin Variants through Two De Novo Protein Design Frameworks
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Discovery of Entry Inhibitors for HIV-1 via a New De Novo Protein Design Framework
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A Flexible Docking Scheme Efficiently Captures the Energetics of Glycan-Cyanovirin Binding
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Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles
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Reconstitution and Engineering of Apoptotic Protein Interactions on the Bacterial Cell Surface
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Rapid Structural Characterization of Human Antibody–Antigen Complexes through Experimentally Validated Computational Docking
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The crystal structure of the dimeric colicin M immunity protein displays a 3D domain swap
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Structural Characterization of Assemblies from Overall Shape and Subcomplex Compositions
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Structural Model of the mAb 806-EGFR Complex Using Computational Docking followed by Computational and Experimental Mutagenesis
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Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains
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A Model for the Solution Structure of the Rod Arrestin Tetramer
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Performance and Its Limits in Rigid Body Protein-Protein Docking
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B-cell epitope mapping for the design of vaccines and effective diagnostics
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An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein–Protein Complexes
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Protein–Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
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Potential Functions for Hydrogen Bonds in Protein Structure Prediction and Design
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Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants
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A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target
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GPC Receptors and Not Ligands Decide the Binding Mode in Neuropeptide Y Multireceptor/Multiligand System
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Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
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Novel class of OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection
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Complete configuration space analysis for structure determination of symmetric homo-oligomers by NMR.
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Bacterial OTU deubiquitinases regulate substrate ubiquitination upon Legionella infection
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