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Protein–protein docking with binding site patch prediction and network‐based terms enhanced combinatorial scoring

https://doi.org/10.1002/prot.22831
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What this work says

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

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Principles of docking: An overview of search algorithms and a guide to scoring functions
inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
inferredcites →https://doi.org/10.1002/prot.20145openalex-snapshot
Hydrophobic complementarity in protein–protein docking
inferredcites →https://doi.org/10.1002/prot.20348openalex-snapshot
Small‐world network approach to identify key residues in protein–protein interaction
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
inferredcites →https://doi.org/10.1002/prot.20559openalex-snapshot
ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5
inferredcites →https://doi.org/10.1002/prot.20563openalex-snapshot
Data‐driven docking: HADDOCK's adventures in CAPRI
inferredcites →https://doi.org/10.1002/prot.20564openalex-snapshot
Performance of the first protein docking server ClusPro in CAPRI rounds 3–5
inferredcites →https://doi.org/10.1002/prot.20570openalex-snapshot
Scoring docking models with evolutionary information
inferredcites →https://doi.org/10.1002/prot.20571openalex-snapshot
Protein–protein docking using 3D‐Dock in rounds 3, 4, and 5 of CAPRI
inferredcites →https://doi.org/10.1002/prot.20577openalex-snapshot
Biologically enhanced sampling geometric docking and backbone flexibility treatment with multiconformational superposition
inferredcites →https://doi.org/10.1002/prot.21396openalex-snapshot
Hot spots—A review of the protein–protein interface determinant amino‐acid residues
inferredcites →https://doi.org/10.1002/prot.21738openalex-snapshot
A filter enhanced sampling and combinatorial scoring study for protein docking in CAPRI
inferredcites →https://doi.org/10.1002/prot.21752openalex-snapshot
A holistic approach to protein docking
inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot
Docking and scoring protein complexes: CAPRI 3rd Edition
inferredcites →https://doi.org/10.1002/prot.21920openalex-snapshot
A combination of rescoring and refinement significantly improves protein docking performance
inferredcites →https://doi.org/10.1006/jmbi.1998.2439openalex-snapshot
The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
inferredcites →https://doi.org/10.1007/s11434-009-0742-xopenalex-snapshot
Network analysis of protein-protein interaction
inferredcites →https://doi.org/10.1016/0022-2836(78)90302-9openalex-snapshot
Computer analysis of protein-protein interaction
inferredcites →https://doi.org/10.1016/j.sbi.2006.03.003openalex-snapshot
High-resolution protein–protein docking
inferredcites →https://doi.org/10.1016/j.sbi.2009.02.008openalex-snapshot
Convergence and combination of methods in protein–protein docking
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
inferredcites →https://doi.org/10.1016/s1097-2765(00)00114-3openalex-snapshot
The Molecular Basis of FHA Domain:Phosphopeptide Binding Specificity and Implications for Phospho-Dependent Signaling Mechanisms
inferredcites →https://doi.org/10.1017/s0033583508004708openalex-snapshot
Protein–protein interaction and quaternary structure
inferredcites →https://doi.org/10.1038/msb4100063openalex-snapshot
Residues crucial for maintaining short paths in network communication mediate signaling in proteins
inferredcites →https://doi.org/10.1038/nsb1203-980openalex-snapshot
Announcing the worldwide Protein Data Bank
inferredcites →https://doi.org/10.1073/pnas.0407280102openalex-snapshot
The modular architecture of protein–protein binding interfaces
inferredcites →https://doi.org/10.1073/pnas.0910756107openalex-snapshot
The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction
inferredcites →https://doi.org/10.1074/jbc.m109.022095openalex-snapshot
The Ternary Structure of the Double-headed Arrowhead Protease Inhibitor API-A Complexed with Two Trypsins Reveals a Novel Reactive Site Conformation
inferredcites →https://doi.org/10.1093/bioinformatics/bti167openalex-snapshot
Topology of small-world networks of protein-protein complex structures
inferredcites →https://doi.org/10.1093/bioinformatics/btm018openalex-snapshot
A simple shape characteristic of protein–protein recognition
inferredcites →https://doi.org/10.1093/bioinformatics/btm303openalex-snapshot
A simple shape characteristic of protein–protein recognition
inferredcites →https://doi.org/10.1093/nar/gkm813openalex-snapshot
HotSprint: database of computational hot spots in protein interfaces
inferredcites →https://doi.org/10.1110/ps.041081905openalex-snapshot
Assessing predictions of protein–protein interaction: The CAPRI experiment
inferredcites →https://doi.org/10.1242/jcs.02369openalex-snapshot
Centaurin-α1 interacts directly with kinesin motor protein KIF13B

What points at this work

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

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Computational Methods for Protein–Protein Interactions
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Blind predictions of protein interfaces by docking calculations in CAPRI
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Ranking multiple docking solutions based on the conservation of inter‐residue contacts
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SVR_CAF: An integrated score function for detecting native protein structures among decoys
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Native fold and docking pose discrimination by the same residue‐based scoring function
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A combinatorial scoring function for protein–RNA docking
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Performance of human and server prediction in CAPRI rounds 38‐45
inferred← citeshttps://doi.org/10.1002/prot.26020openalex-snapshot
Simplified geometric representations of protein structures identify complementary interaction interfaces
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Analysis of Protein Structures Using Residue Interaction Networks
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Prediction of Biomolecular Complexes
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CoDockPP: A Multistage Approach for Global and Site-Specific Protein–Protein Docking
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GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations
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Structural basis for recognition of an endogenous peptide by the plant receptor kinase PEPR1
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Structural basis for specific self-incompatibility response in Brassica
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Modulation of BIN2 kinase activity by HY5 controls hypocotyl elongation in the light
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Nicking mechanism underlying the DNA phosphorothioate-sensing antiphage defense by SspE
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CdS quantum dot sensitized anatase TiO2 hierarchical nanostructures for photovoltaic application
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Protein–protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction
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Thermodynamics and mechanism of afatinib–EGFR binding through a QM/MM approach
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Molecular Mechanism for Inhibition of a Critical Component in the Arabidopsis thaliana Abscisic Acid Signal Transduction Pathways, SnRK2.6, by Protein Phosphatase ABI1
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The E3 ubiquitin ligase SCFFBXL14 complex stimulates neuronal differentiation by targeting the Notch signaling factor HES1 for proteolysis
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Molecular docking study on vitamin D supplements to understand their interaction with VDR-RXRα heterodimer and VDRE of TAGAP gene
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Conformational Dynamics of the D53−D3−D14 Complex in Strigolactone Signaling
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HawkRank: a new scoring function for protein–protein docking based on weighted energy terms
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Faculty Opinions recommendation of Modulation of BIN2 kinase activity by HY5 controls hypocotyl elongation in the light.
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