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Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6–12
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Structure of the binding site for inositol phosphates in a PH domain.
inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
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Protein–protein docking predictions for the CAPRI experiment
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Assessment of blind predictions of protein–protein interactions: Current status of docking methods
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Modeling structurally variable regions in homologous proteins with rosetta
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CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock
inferredcites →https://doi.org/10.1002/prot.20556openalex-snapshot
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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Data‐driven docking: HADDOCK's adventures in CAPRI
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Docking prediction using biological information, ZDOCK sampling technique, and clustering guided by the DFIRE statistical energy function
inferredcites →https://doi.org/10.1002/prot.20577openalex-snapshot
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition
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Improved beta‐protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
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Local motions in a benchmark of allosteric proteins
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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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Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions
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Regulation of Smurf2 Ubiquitin Ligase Activity by Anchoring the E2 to the HECT Domain
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Molecular Basis for Bacterial Class I Release Factor Methylation by PrmC
inferredcites →https://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot
High-resolution protein–protein docking
inferredcites →https://doi.org/10.1016/j.str.2004.09.014openalex-snapshot
Complementarity of Structure Ensembles in Protein-Protein Binding
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Structural Model of the mAb 806-EGFR Complex Using Computational Docking followed by Computational and Experimental Mutagenesis
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
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Structural Basis for Activation of ARF GTPase
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Structure of the Escherichia coli TolB protein determined by MAD methods at 1.95 Å resolution
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Bacterial Polypeptide Release Factor RF2 Is Structurally Distinct from Eukaryotic eRF1
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Conformational Flexibility Underlies Ubiquitin Ligation Mediated by the WWP1 HECT Domain E3 Ligase
inferredcites →https://doi.org/10.1021/bi034026popenalex-snapshot
Structures along the Catalytic Pathway of PrmC/HemK, an N 5 -Glutamine AdoMet-Dependent Methyltransferase
inferredcites →https://doi.org/10.1021/ja070153nopenalex-snapshot
Molecular Mimicry Enables Competitive Recruitment by a Natively Disordered Protein
inferredcites →https://doi.org/10.1038/ncb1244openalex-snapshot
Golgi-localized GAP for Cdc42 functions downstream of ARF1 to control Arp2/3 complex and F-actin dynamics
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Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
inferredcites →https://doi.org/10.1038/nsmb903openalex-snapshot
SUMO modification of the ubiquitin-conjugating enzyme E2-25K
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Structural basis of the Sir1–origin recognition complex interaction in transcriptional silencing
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A simple physical model for binding energy hot spots in protein–protein complexes
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Crystal Structure of Murine/Human Ubc9 Provides Insight into the Variability of the Ubiquitin-conjugating System
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Identification of a Substrate Recognition Site on Ubc9
inferredcites →https://doi.org/10.1093/emboj/21.4.769openalex-snapshot
The hemK gene in Escherichia coli encodes the N5‐glutamine methyltransferase that modifies peptide release factors
inferredcites →https://doi.org/10.1093/emboj/cdf468openalex-snapshot
Structure and function of the BAH‐containing domain of Orc1p in epigenetic silencing
inferredcites →https://doi.org/10.1093/nar/gkh468openalex-snapshot
Protein structure prediction and analysis using the Robetta server
inferredcites →https://doi.org/10.1093/protein/12.4.271openalex-snapshot
An analysis of conformational changes on protein–protein association: implications for predictive docking
inferredcites →https://doi.org/10.1110/ps.0242703openalex-snapshot
Cyclic coordinate descent: A robotics algorithm for protein loop closure
inferredcites →https://doi.org/10.1110/ps.041222905openalex-snapshot
Improved side‐chain modeling for protein–protein docking
inferredcites →https://doi.org/10.1126/science.286.5443.1321openalex-snapshot
Structure of an E6AP-UbcH7 Complex: Insights into Ubiquitination by the E2-E3 Enzyme Cascade
inferredcites →https://doi.org/10.1126/stke.2192004pl2openalex-snapshot
Computational Alanine Scanning of Protein-Protein Interfaces
inferredcites →https://doi.org/10.1128/jb.182.3.821-824.2000openalex-snapshot
Identification by Genetic Suppression of Escherichia coli TolB Residues Important for TolB-Pal Interaction
inferredcites →https://doi.org/10.1128/mcb.24.2.774-786.2004openalex-snapshot
The Origin Recognition Complex and Sir4 Protein Recruit Sir1p to Yeast Silent Chromatin through Independent Interactions Requiring a Common Sir1p Domain
inferredcites →https://doi.org/10.2210/pdb1oap/pdbopenalex-snapshot
Mad structure of the periplasmique domain of the Escherichia coli PAL protein
inferredcites →https://doi.org/10.2970/tpdb.2007.61openalex-snapshot
Ubiquitin-conjugating enzyme E2-25 kDa
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking
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A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13–19
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Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27
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Interolog interfaces in protein–protein docking
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Docking With Rosetta and Deep Learning Approaches in CAPRI Rounds 47–55
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Approaches to Backbone Flexibility in Protein–Protein Docking
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Analysis and Prediction of Protein Quaternary Structure
inferred← citeshttps://doi.org/10.1007/978-1-61779-588-6_13openalex-snapshot
Methods for the Homology Modeling of Antibody Variable Regions
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Molecular Dynamic and Docking Interaction Study of Heterodera glycines Serine Proteinase with Vigna mungo Proteinase Inhibitor
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Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles
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A neutralizing recombinant single chain antibody, scFv, against BaP1, A P-I hemorrhagic metalloproteinase from Bothrops asper snake venom
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Protein–protein interaction and quaternary structure
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CoDockPP: A Multistage Approach for Global and Site-Specific Protein–Protein Docking
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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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Molecular docking and molecular dynamics simulation studies on the adsorption/desorption behavior of bone morphogenetic protein-7 on the β-tricalcium phosphate surface
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Mechanism of Polyubiquitin Chain Recognition by the Human Ubiquitin Conjugating Enzyme Ube2g2
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Efficient flexible backbone protein–protein docking for challenging targets
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The RosettaDock server for local protein-protein docking
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Quantitative Predictions of Binding Free Energy Changes in Drug-Resistant Influenza Neuraminidase
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Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2
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