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Template‐based modeling and ab‐initio docking using CoDock 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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CAPRI: A Critical Assessment of PRedicted Interactions

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ZDOCK: An initial‐stage protein‐docking algorithm

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An iterative knowledge‐based scoring function for protein–protein recognition

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Global and local structural similarity in protein–protein complexes: Implications for template‐based docking

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Docking, scoring, and affinity prediction in CAPRI

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Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment

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Solution structure of the lymphocyte receptor Nkrp1a reveals a distinct conformation of the long loop region as compared to in the crystal structure

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Template‐based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30

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Modeling protein assemblies: Critical Assessment of Predicted Interactions (CAPRI) 15 years hence.

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Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking

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The challenge of modeling protein assemblies: the CASP12‐CAPRI experiment

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Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment

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The crystal structure of a liganded trehalose/maltose-binding protein from the hyperthermophilic archaeon Thermococcus litoralis at 1.85 Å

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Structural basis of diverse sequence-dependent target recognition by the 8 kDa dynein light chain11Edited by P. E. Wright

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Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking

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Molecular architecture of mouse activating NKR-P1 receptors

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High-resolution protein–protein docking by global optimization: recent advances and future challenges

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Protein-Protein Interfaces Are Special

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CoDockPP: A Multistage Approach for Global and Site-Specific Protein–Protein Docking

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Crystal Structure of the Acid-Induced Arginine Decarboxylase from Escherichia coli : Reversible Decamer Assembly Controls Enzyme Activity

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CEACAM1 regulates TIM-3-mediated tolerance and exhaustion

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Helicobacter pylori adhesin HopQ engages in a virulence-enhancing interaction with human CEACAMs

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Structure to function of an α-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis

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Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space

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Structural insights into the Escherichia coli lysine decarboxylases and molecular determinants of interaction with the AAA+ ATPase RavA

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Crystal structure of an inverting GH 43 1,5-α- L -arabinanase from Geobacillus stearothermophilus complexed with its substrate

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Structural and thermodynamic characterization of a cytoplasmic dynein light chain–intermediate chain complex

inferredcites →https://doi.org/10.1073/pnas.89.6.2195openalex-snapshot

Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

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Multivalency in the Assembly of Intrinsically Disordered Dynein Intermediate Chain

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Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states

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Helicobacter pylori adhesin HopQ disrupts trans dimerization in human CEACAMs

What points at this work

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

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Characteristic of Docking Cavities

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Review and Comparative Analysis of Methods and Advancements in Predicting Protein Complex Structure

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Enhancing Protein Function Prediction Performance by Utilizing AlphaFold-Predicted Protein Structures

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Evaluation of Angiotensin-Converting Enzyme 2 Expression In Vivo with Novel 68Ga-Labeled Peptides Originated from the Coronavirus Receptor-Binding Domain

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Protective role of serpina3c as a novel thrombin inhibitor against atherosclerosis in mice

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MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm

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CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction

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Advances in bioinformatics and multi-omics integration: transforming viral infectious disease research in veterinary medicine

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Applications of Bioinformatics on Genomics and Proteomics Levels Highlighted in Brucella Pathogen

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The Use of Molecular Dynamics Simulation Method to Quantitatively Evaluate the Affinity between HBV Antigen T Cell Epitope Peptides and HLA-A Molecules

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Single-Disulfide Conopeptide Czon1107, an Allosteric Antagonist of the Human α3β4 Nicotinic Acetylcholine Receptor

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