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Data‐driven docking: HADDOCK's adventures in CAPRI
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Cohesin-dockerin recognition in cellulosome assembly: Experiment versus hypothesis
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Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
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Refinement of protein structures in explicit solvent
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CAPRI: A Critical Assessment of PRedicted Interactions
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Prediction of protein interaction sites from sequence profile and residue neighbor list
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The impact of protein flexibility on protein–protein docking
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A calculation strategy for the structure determination of symmetric demers by 1H NMR
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A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform 1 1Edited by M. Yaniv
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GROMACS 3.0: a package for molecular simulation and trajectory analysis
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Antigenicity and immunogenicity of P30-derived peptides in experimental models of toxoplasmosis
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Epitopic analysis of the Toxoplasma gondii major surface antigen SAG1
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Properties of TAXI-type endoxylanase inhibitors
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Molecular Organization of a Recombinant Subviral Particle from Tick-Borne Encephalitis Virus
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Cleavage of Colicin D Is Necessary for Cell Killing and Requires the Inner Membrane Peptidase LepB
inferredcites →https://doi.org/10.1017/s0031182001008460openalex-snapshot
Anti-SAG1 peptide antibodies inhibit the penetration ofToxoplasma gondiitachyzoites into enterocyte cell lines
inferredcites →https://doi.org/10.1021/bi011853mopenalex-snapshot
Duplicated Dockerin Subdomains of Clostridium thermocellum Endoglucanase CelD Bind to a Cohesin Domain of the Scaffolding Protein CipA with Distinct Thermodynamic Parameters and a Negative Cooperativity
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Mapping by Site-Directed Mutagenesis of the Region Responsible for Cohesin−Dockerin Interaction on the Surface of the Seventh Cohesin Domain of Clostridium thermocellum CipA
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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1038/36337openalex-snapshot
Prion (PrPSc)-specific epitope defined by a monoclonal antibody
inferredcites →https://doi.org/10.1038/nature02582openalex-snapshot
Structural basis of protein phosphatase 1 regulation
inferredcites →https://doi.org/10.1038/sj.emboj.7600064openalex-snapshot
Structure of a flavivirus envelope glycoprotein in its low‐pH‐induced membrane fusion conformation
inferredcites →https://doi.org/10.1038/sj.emboj.7600162openalex-snapshot
Structural inhibition of the colicin D tRNase by the tRNA‐mimicking immunity protein
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Study of the subunit interactions in myosin phosphatase by surface plasmon resonance
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Insight into the PrP C → PrP Sc conversion from the structures of antibody-bound ovine prion scrapie-susceptibility variants
inferredcites →https://doi.org/10.1073/pnas.0401942101openalex-snapshot
Anchor residues in protein–protein interactions
inferredcites →https://doi.org/10.1073/pnas.1936124100openalex-snapshot
Cellulosome assembly revealed by the crystal structure of the cohesin–dockerin complex
inferredcites →https://doi.org/10.1073/pnas.97.15.8334openalex-snapshot
NMR structure of the bovine prion protein
inferredcites →https://doi.org/10.1074/jbc.272.6.3683openalex-snapshot
Interactions of the Subunits of Smooth Muscle Myosin Phosphatase
inferredcites →https://doi.org/10.1074/jbc.m009237200openalex-snapshot
Cohesin-Dockerin Interaction in Cellulosome Assembly
inferredcites →https://doi.org/10.1074/jbc.m404212200openalex-snapshot
Structural Basis for Inhibition of Aspergillus niger Xylanase by Triticum aestivum Xylanase Inhibitor-I
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Homology modeling, model and software evaluation: three related resources.
inferredcites →https://doi.org/10.1093/emboj/16.8.1876openalex-snapshot
Structural basis for the recognition of regulatory subunits by the catalytic subunit of protein phosphatase 1
inferredcites →https://doi.org/10.1093/nar/gkg520openalex-snapshot
SWISS-MODEL: an automated protein homology-modeling server
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Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination
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Data‐driven docking for the study of biomolecular complexes
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Structural requirements for low-pH-induced rearrangements in the envelope glycoprotein of tick-borne encephalitis virus
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Mapping of Functional Elements in the Stem-Anchor Region of Tick-Borne Encephalitis Virus Envelope Protein E
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Mutational Evidence for an Internal Fusion Peptide in Flavivirus Envelope Protein E
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Membrane Interactions of the Tick-Borne Encephalitis Virus Fusion Protein E at Low pH
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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WHISCY: What information does surface conservation yield? Application to data‐driven docking
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Scoring a diverse set of high‐quality docked conformations: A metascore based on electrostatic and desolvation interactions
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Flexible relaxation of rigid‐body docking solutions
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Constructing ensembles of flexible fragments in native proteins by iterative stochastic elimination is relevant to protein–protein interfaces
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Implicit flexibility in protein docking: Cross‐docking and local refinement
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HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
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Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6–12
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Protein–protein docking: Progress in CAPRI rounds 6–12 using a combination of methods: The introduction of steered solvated molecular dynamics
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A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI
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A holistic approach to protein docking
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Selection of near‐native poses in CAPRI rounds 13‐19
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Strengths and weaknesses of data‐driven docking in critical assessment of prediction of interactions
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Protein–protein docking with binding site patch prediction and network‐based terms enhanced combinatorial scoring
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Optimized grid‐based protein–protein docking as a global search tool followed by incorporating experimentally derivable restraints
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Defining the limits of homology modeling in information‐driven protein docking
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Performance of ZDOCK in CAPRI rounds 20–26
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Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB
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Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1
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Ab initio fragment molecular orbital calculations on specific interactions between aryl hydrocarbon receptor and dioxin
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Multiscale Protein and Peptide Docking
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Use of Residual Dipolar Couplings in Structural Analysis of Protein-Ligand Complexes by Solution NMR Spectroscopy
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Analysis and Prediction of Protein Quaternary Structure
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Prediction of Protein-Protein Binding Interfaces
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Nucleotide docking: prediction of reactant state complexes for ribonuclease enzymes
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Predicting functional residues of the Solanum lycopersicum aspartic protease inhibitor (SLAPI) by combining sequence and structural analysis with molecular docking
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WeNMR: Structural Biology on the Grid
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Conformer Selection and Induced Fit in Flexible Backbone Protein–Protein Docking Using Computational and NMR Ensembles
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Rapid Structural Characterization of Human Antibody–Antigen Complexes through Experimentally Validated Computational Docking
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Robust Antibody–Antigen Complexes Prediction Generated by Combining Sequence Analyses, Mutagenesis, In Vitro Evolution, X-ray Crystallography and In Silico Docking
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Specific interactions between aryl hydrocarbon receptor and dioxin congeners: Ab initio fragment molecular orbital calculations
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Macromolecular docking restrained by a small angle X-ray scattering profile
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Prediction of protein–protein interaction sites using patch-based residue characterization
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