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Combining interface core and whole interface descriptors in postscan processing of protein‐protein docking models

https://doi.org/10.1002/prot.22436
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What this work says

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

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Shape complementarity at protein–protein interfaces
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Docking unbound proteins using shape complementarity, desolvation, and electrostatics
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Welcome to CAPRI: A Critical Assessment of PRedicted Interactions
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CAPRI: A Critical Assessment of PRedicted Interactions
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Weighted geometric docking: Incorporating external information in the rotation‐translation scan
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Assessment of blind predictions of protein–protein interactions: Current status of docking methods
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Dissecting subunit interfaces in homodimeric proteins
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Combination of scoring functions improves discrimination in protein–protein docking
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Hydrophobic complementarity in protein–protein docking
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Statistical analysis and prediction of protein–protein interfaces
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Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
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The targets of CAPRI rounds 3–5
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Classification of protein complexes based on docking difficulty
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Docking to single‐domain and multiple‐domain proteins: Old and new challenges
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Protein–protein docking benchmark 2.0: An update
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PIPER: An FFT‐based protein docking program with pairwise potentials
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A protein‐specifically adapted scoring function for the reranking of docking solutions
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Comprehensive statistical analysis of residues interaction specificity at protein–protein interfaces
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ZRANK: Reranking protein docking predictions with an optimized energy function
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Hot spots—A review of the protein–protein interface determinant amino‐acid residues
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pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking
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Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines
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The targets of CAPRI rounds 6–12
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Shape Complementarity at Protein/Protein Interfaces
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Electrostatic complementarity at protein/protein interfaces 1 1Edited by B. Honig
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Analysis of protein-protein interaction sites using surface patches 1 1Edited by G.Von Heijne
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Anatomy of hot spots in protein interfaces
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The atomic structure of protein-protein recognition sites 1 1Edited by A. R. Fersht
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An Antibody That Prevents the Hemagglutinin Low pH Fusogenic Transition
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The interface of protein-protein complexes: Analysis of contacts and prediction of interactions
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Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces
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Characterization of Protein–Protein Interfaces
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Complex-type-dependent scoring functions in protein–protein docking
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On proteins, grids, correlations, and docking
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A Dissection of Specific and Non-specific Protein–Protein Interfaces
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The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein–Protein Complexes with an Application to Protein–Protein Docking
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Crystal Structure of the Complex between the Monomeric Form of Toxoplasma gondii Surface Antigen 1 (SAG1) and a Monoclonal Antibody that Mimics the Human Immune Response
inferredcites →https://doi.org/10.1016/j.jmb.2007.03.077openalex-snapshot
Structural Basis for the Bifunctionality of the U5 snRNP 52K Protein (CD2BP2)
inferredcites →https://doi.org/10.1016/j.jmb.2007.05.022openalex-snapshot
Inference of Macromolecular Assemblies from Crystalline State
inferredcites →https://doi.org/10.1016/j.jmb.2008.05.034openalex-snapshot
Structural and Mutational Analyses of the Interaction between the Barley α-Amylase/Subtilisin Inhibitor and the Subtilisin Savinase Reveal a Novel Mode of Inhibition
inferredcites →https://doi.org/10.1016/j.sbi.2006.02.002openalex-snapshot
Flexible protein–protein docking
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.2007.10.025openalex-snapshot
Structure of the Yeast tRNA m7G Methylation Complex
inferredcites →https://doi.org/10.1016/s0006-3495(03)74997-2openalex-snapshot
Development of Unified Statistical Potentials Describing Protein-Protein Interactions
inferredcites →https://doi.org/10.1016/s0021-9258(17)46181-3openalex-snapshot
The structure of protein-protein recognition sites.
inferredcites →https://doi.org/10.1016/s0022-2836(02)01223-8openalex-snapshot
Analysing Six Types of Protein–Protein Interfaces
inferredcites →https://doi.org/10.1016/s0022-2836(02)01281-0openalex-snapshot
Structural Characterisation and Functional Significance of Transient Protein–Protein Interactions
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/s0065-3233(02)61001-0openalex-snapshot
Structural basis of macromolecular recognition
inferredcites →https://doi.org/10.1016/s0079-6107(96)00001-6openalex-snapshot
Protein-protein recognition
inferredcites →https://doi.org/10.1016/s0959-440x(00)00065-8openalex-snapshot
Electrostatic aspects of protein–protein interactions
inferredcites →https://doi.org/10.1016/s0959-440x(03)00064-2openalex-snapshot
Genome-wide studies of protein–protein interaction
inferredcites →https://doi.org/10.1016/s0959-440x(98)80047-xopenalex-snapshot
Predictive docking of protein—protein and protein—DNA complexes
inferredcites →https://doi.org/10.1016/s0969-2126(02)00759-1openalex-snapshot
Structures of Two Streptococcal Superantigens Bound to TCR β Chains Reveal Diversity in the Architecture of T Cell Signaling Complexes
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Molecular Mimicry Enables Competitive Recruitment by a Natively Disordered Protein
inferredcites →https://doi.org/10.1038/nature01873openalex-snapshot
Complex between nidogen and laminin fragments reveals a paradigmatic β-propeller interface
inferredcites →https://doi.org/10.1038/nature02582openalex-snapshot
Structural basis of protein phosphatase 1 regulation
inferredcites →https://doi.org/10.1038/sj.emboj.7600162openalex-snapshot
Structural inhibition of the colicin D tRNase by the tRNA‐mimicking immunity protein
inferredcites →https://doi.org/10.1038/sj.emboj.7601634openalex-snapshot
Structural basis for ARF1‐mediated recruitment of ARHGAP21 to Golgi membranes
inferredcites →https://doi.org/10.1073/pnas.0400014101openalex-snapshot
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.0502667102openalex-snapshot
Structure, function, and evolution of transient and obligate protein–protein interactions
inferredcites →https://doi.org/10.1073/pnas.0503525102openalex-snapshot
Structural basis of the Sir1–origin recognition complex interaction in transcriptional silencing
inferredcites →https://doi.org/10.1073/pnas.0505425102openalex-snapshot
Conservation and relative importance of residues across protein-protein interfaces
inferredcites →https://doi.org/10.1073/pnas.0611173104openalex-snapshot
Evidence for a dual binding mode of dockerin modules to cohesins
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.89.6.2195openalex-snapshot
Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.
inferredcites →https://doi.org/10.1073/pnas.93.1.13openalex-snapshot
Principles of protein-protein interactions.
inferredcites →https://doi.org/10.1073/pnas.95.11.5913openalex-snapshot
A unified statistical framework for sequence comparison and structure comparison
inferredcites →https://doi.org/10.1074/jbc.m202327200openalex-snapshot
Three Camelid VHH Domains in Complex with Porcine Pancreatic α-Amylase
inferredcites →https://doi.org/10.1074/jbc.m404212200openalex-snapshot
Structural Basis for Inhibition of Aspergillus niger Xylanase by Triticum aestivum Xylanase Inhibitor-I
inferredcites →https://doi.org/10.1074/jbc.m404225200openalex-snapshot
The Dual Nature of the Wheat Xylanase Protein Inhibitor XIP-I
inferredcites →https://doi.org/10.1074/jbc.m703800200openalex-snapshot
Binding of Rac1, Rnd1, and RhoD to a Novel Rho GTPase Interaction Motif Destabilizes Dimerization of the Plexin-B1 Effector Domain
inferredcites →https://doi.org/10.1093/bioinformatics/btl079openalex-snapshot
Predicting protein interaction sites: binding hot-spots in protein–protein and protein–ligand interfaces
inferredcites →https://doi.org/10.1093/bioinformatics/btl524openalex-snapshot
Inherent limitations in protein–protein docking procedures
inferredcites →https://doi.org/10.1093/bioinformatics/btl654openalex-snapshot
A new protein–protein docking scoring function based on interface residue properties
inferredcites →https://doi.org/10.1093/bioinformatics/btn022openalex-snapshot
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein–protein interactions
inferredcites →https://doi.org/10.1093/emboj/cdg359openalex-snapshot
Diversity of protein–protein interactions
inferredcites →https://doi.org/10.1093/protein/13.2.77openalex-snapshot
Protein domain interfaces: characterization and comparison with oligomeric protein interfaces
inferredcites →https://doi.org/10.1110/ps.062245906openalex-snapshot
Revisiting the Voronoi description of protein–protein interfaces
inferredcites →https://doi.org/10.1110/ps.062405906openalex-snapshot
Prediction of residues in discontinuous B‐cell epitopes using protein 3D structures
inferredcites →https://doi.org/10.1110/ps.26002openalex-snapshot
Electrostatics in protein–protein docking
inferredcites →https://doi.org/10.1110/ps.8.3.603openalex-snapshot
Comparison of protein–protein interactions in serine protease‐inhibitor and antibody‐antigen complexes: Implications for the protein docking problem
inferredcites →https://doi.org/10.1111/j.1742-4658.2004.04473.xopenalex-snapshot
Data‐driven docking for the study of biomolecular complexes
inferredcites →https://doi.org/10.1186/1471-2105-7-27openalex-snapshot
NOXclass: prediction of protein-protein interaction types
inferredcites →https://doi.org/10.1186/1472-6807-5-15openalex-snapshot
Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different
inferredcites →https://doi.org/10.51936/noqf3710openalex-snapshot
ROC curve, lift chart and calibration plot

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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Scoring optimisation of unbound protein–protein docking including protein binding site predictions
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Integrating atom‐based and residue‐based scoring functions for protein–protein docking
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CAPRI targets T29–T42: Proving ground for new docking procedures
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Great interactions: How binding incorrect partners can teach us about protein recognition and function
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Prediction of Biomolecular Complexes
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Search strategies and evaluation in protein–protein docking: principles, advances and challenges
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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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Elucidating Substrate and Inhibitor Binding Sites on the Surface of GSK-3β and the Refinement of a Competitive Inhibitor
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Monoclonal antibody MN423 as a stable mold facilitates structure determination of disordered tau protein
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The Autophagy Protein Atg12 Associates with Antiapoptotic Bcl-2 Family Members to Promote Mitochondrial Apoptosis
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Accounting for conformational changes during protein–protein docking
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Lupus-associated causal mutation in neutrophil cytosolic factor 2 (NCF2) brings unique insights to the structure and function of NADPH oxidase
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Systemic Lupus Erythematosus-associated Neutrophil Cytosolic Factor 2 Mutation Affects the Structure of NADPH Oxidase Complex
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Molecular Mechanisms and Kinetic Effects of FXYD1 and Phosphomimetic Mutants on Purified Human Na,K-ATPase
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Determination of an effective scoring function for RNA–RNA interactions with a physics-based double-iterative method
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Conformation-Specific Inhibitory Anti-MMP-7 Monoclonal Antibody Sensitizes Pancreatic Ductal Adenocarcinoma Cells to Chemotherapeutic Cell Kill
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Faculty Opinions recommendation of Lupus-associated causal mutation in neutrophil cytosolic factor 2 (NCF2) brings unique insights to the structure and function of NADPH oxidase.
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Flexible Protein-Protein Docking
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