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Ranking multiple docking solutions based on the conservation of inter‐residue contacts

https://doi.org/10.1002/prot.24314
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What this work says

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

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Scoring docked conformations generated by rigid-body protein-protein docking
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Using correlated parameters for improved ranking of protein–protein docking decoys
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PROCOS: Computational analysis of protein–protein complexes
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Assessment of blind predictions of protein–protein interactions: Current status of docking methods
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Scoring docking models with evolutionary information
inferredcites →https://doi.org/10.1002/prot.21373openalex-snapshot
ZRANK: Reranking protein docking predictions with an optimized energy function
inferredcites →https://doi.org/10.1002/prot.21419openalex-snapshot
pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking
inferredcites →https://doi.org/10.1002/prot.21495openalex-snapshot
FireDock: Fast interaction refinement in molecular docking
inferredcites →https://doi.org/10.1002/prot.21603openalex-snapshot
Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines
inferredcites →https://doi.org/10.1002/prot.21679openalex-snapshot
Electrostatic rate enhancement and transient complex of protein–protein association
inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot
Docking and scoring protein complexes: CAPRI 3rd Edition
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An iterative knowledge‐based scoring function for protein–protein recognition
inferredcites →https://doi.org/10.1002/prot.21968openalex-snapshot
Specific interactions for ab initio folding of protein terminal regions with secondary structures
inferredcites →https://doi.org/10.1002/prot.22252openalex-snapshot
Consensus scoring for enriching near‐native structures from protein–protein docking decoys
inferredcites →https://doi.org/10.1002/prot.22764openalex-snapshot
Performance of ZDOCK and ZRANK in CAPRI rounds 13–19
inferredcites →https://doi.org/10.1002/prot.22770openalex-snapshot
Detection and refinement of encounter complexes for protein–protein docking: Taking account of macromolecular crowding
inferredcites →https://doi.org/10.1002/prot.22774openalex-snapshot
The targets of CAPRI Rounds 13–19
inferredcites →https://doi.org/10.1002/prot.22818openalex-snapshot
Docking and scoring protein interactions: CAPRI 2009
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Protein–protein docking with binding site patch prediction and network‐based terms enhanced combinatorial scoring
inferredcites →https://doi.org/10.1002/prot.22850openalex-snapshot
Blind predictions of protein interfaces by docking calculations in CAPRI
inferredcites →https://doi.org/10.1002/prot.24078openalex-snapshot
Clustering biomolecular complexes by residue contacts similarity
inferredcites →https://doi.org/10.1002/prot.24110openalex-snapshot
Scoring protein interaction decoys using exposed residues (SPIDER): A novel multibody interaction scoring function based on frequent geometric patterns of interfacial residues
inferredcites →https://doi.org/10.1016/j.str.2007.06.007openalex-snapshot
The Third CAPRI Assessment Meeting Toronto, Canada, April 20–21, 2007
inferredcites →https://doi.org/10.1016/s0006-3495(97)78838-6openalex-snapshot
Simulation of the diffusional association of barnase and barstar
inferredcites →https://doi.org/10.1016/s0006-3495(99)77281-4openalex-snapshot
Free Energy Landscapes of Encounter Complexes in Protein-Protein Association
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/10.1021/ja070153nopenalex-snapshot
Molecular Mimicry Enables Competitive Recruitment by a Natively Disordered Protein
inferredcites →https://doi.org/10.1021/jp2120143openalex-snapshot
Combining Statistical Potentials with Dynamics-Based Entropies Improves Selection from Protein Decoys and Docking Poses
inferredcites →https://doi.org/10.1038/msb.2011.3openalex-snapshot
Towards the prediction of protein interaction partners using physical docking
inferredcites →https://doi.org/10.1038/nature05201openalex-snapshot
Visualization of transient encounter complexes in protein–protein association
inferredcites →https://doi.org/10.1038/nature05306openalex-snapshot
Brief encounters bolster contacts
inferredcites →https://doi.org/10.1073/pnas.95.19.11158openalex-snapshot
Clustering of low-energy conformations near the native structures of small proteins
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/btn497openalex-snapshot
D ockground protein–protein docking decoy set
inferredcites →https://doi.org/10.1093/bioinformatics/btr484openalex-snapshot
COCOMAPS: a web application to analyze and visualize contacts at the interface of biomolecular complexes
inferredcites →https://doi.org/10.1093/nar/28.1.235openalex-snapshot
The Protein Data Bank
inferredcites →https://doi.org/10.1186/1471-2105-12-280openalex-snapshot
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking
inferredcites →https://doi.org/10.1186/1471-2105-13-s4-s19openalex-snapshot
CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions
inferredcites →https://doi.org/10.1371/journal.pone.0018541openalex-snapshot
A Collaborative Filtering Approach for Protein-Protein Docking Scoring Functions

What points at this work

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

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Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study
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Increasing the fraction of correct solutions in ensembles of protein–protein docking models by an iterative consensus algorithm
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Using a consensus approach based on the conservation of inter‐residue contacts to rank CAPRI models
inferred← citeshttps://doi.org/10.1002/prot.24425openalex-snapshot
Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20–27
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Performance of ZDOCK in CAPRI rounds 20–26
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A machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison
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Rigid-Docking Approaches to Explore Protein–Protein Interaction Space
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Prediction of Biomolecular Complexes
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Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design
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Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues
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Molecular Dynamics Characterization of Five Pathogenic Factor X Mutants Associated with Decreased Catalytic Activity
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Reliability analysis and optimization of the consensus docking approach for the development of virtual screening studies
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A random forest classifier for protein–protein docking models
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Improving classification of correct and incorrect protein–protein docking models by augmenting the training set
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CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts
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Progress in small-angle scattering from biological solutions at high-brilliance synchrotrons
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Identification of shared tumor epitopes from endogenous retroviruses inducing high-avidity cytotoxic T cells for cancer immunotherapy
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The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses
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Structural Basis for the Recognition in an Idiotype-Anti-Idiotype Antibody Complex Related to Celiac Disease
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OncoBinder facilitates interpretation of proteomic interaction data by capturing coactivation pairs in cancer
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Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study
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Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein–Protein Docking Poses
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A Combined Spectroscopic and In Silico Approach to Evaluate the Interaction of Human Frataxin with Mitochondrial Superoxide Dismutase
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Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps
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Immunoinformatics-Aided Design of a Peptide Based Multiepitope Vaccine Targeting Glycoproteins and Membrane Proteins against Monkeypox Virus
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Additional file 1 of The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses
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Contacts-based prediction of binding affinity in protein–protein complexes
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