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Using a consensus approach based on the conservation of inter‐residue contacts to rank CAPRI models
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/1097-0134(20000815)40:3<525::aid-prot190>3.0.co;2-fopenalex-snapshot
Scoring docked conformations generated by rigid-body protein-protein docking
inferredcites →https://doi.org/10.1002/anie.201208688openalex-snapshot
Probing Target Search Pathways during Protein–Protein Association by Rational Mutations Based on Paramagnetic Relaxation Enhancement
inferredcites →https://doi.org/10.1002/prot.10393openalex-snapshot
Assessment of blind predictions of protein–protein interactions: Current status of docking methods
inferredcites →https://doi.org/10.1002/prot.21669openalex-snapshot
Assessment of predictions in the model quality assessment category
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.21736openalex-snapshot
Assessing the energy landscape of CAPRI targets by FunHunt
inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot
Docking and scoring protein complexes: CAPRI 3rd Edition
inferredcites →https://doi.org/10.1002/prot.21930openalex-snapshot
The size of the intermolecular energy funnel in protein–protein interactions
inferredcites →https://doi.org/10.1002/prot.21997openalex-snapshot
Discrimination of near‐native structures in protein–protein docking by testing the stability of local minima
inferredcites →https://doi.org/10.1002/prot.22534openalex-snapshot
Evaluation of CASP8 model quality predictions
inferredcites →https://doi.org/10.1002/prot.22726openalex-snapshot
Self-association of TPR domains: Lessons learned from a designed, consensus-based TPR oligomer
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.22818openalex-snapshot
Docking and scoring protein interactions: CAPRI 2009
inferredcites →https://doi.org/10.1002/prot.23180openalex-snapshot
Evaluation of model quality predictions in CASP9
inferredcites →https://doi.org/10.1002/prot.24078openalex-snapshot
Clustering biomolecular complexes by residue contacts similarity
inferredcites →https://doi.org/10.1002/prot.24314openalex-snapshot
Ranking multiple docking solutions based on the conservation of inter‐residue contacts
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/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/s0969-2126(03)00076-5openalex-snapshot
Design of Stable α-Helical Arrays from an Idealized TPR Motif
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/10.1039/c005060copenalex-snapshot
Protein–protein docking tested in blind predictions: the CAPRI experiment
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/btl395openalex-snapshot
Solvated docking: introducing water into the modelling of biomolecular complexes
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/gkr176openalex-snapshot
Mechanism of activation of methyltransferases involved in translation by the Trm112 ‘hub’ protein
inferredcites →https://doi.org/10.1110/ps.8.6.1181openalex-snapshot
Folding funnels, binding funnels, and protein function
inferredcites →https://doi.org/10.1110/ps.8701openalex-snapshot
How common is the funnel‐like energy landscape in protein‐protein interactions?
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/10.1529/biophysj.108.132977openalex-snapshot
Chasing Funnels on Protein-Protein Energy Landscapes at Different Resolutions
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/pro.70314openalex-snapshot
Increasing the fraction of correct solutions in ensembles of protein–protein docking models by an iterative consensus algorithm
inferred← citeshttps://doi.org/10.1007/978-1-0716-2617-7_4openalex-snapshot
Modeling Protein Complexes and Molecular Assemblies Using Computational Methods
inferred← citeshttps://doi.org/10.1007/978-94-024-1069-3_8openalex-snapshot
Prediction of Biomolecular Complexes
inferred← citeshttps://doi.org/10.1007/s12033-024-01119-4openalex-snapshot
Importance of Inter-residue Contacts for Understanding Protein Folding and Unfolding Rates, Remote Homology, and Drug Design
inferred← citeshttps://doi.org/10.1016/j.jsb.2016.03.008openalex-snapshot
Analysis of the interface variability in NMR structure ensembles of protein–protein complexes
inferred← citeshttps://doi.org/10.1021/bi500770popenalex-snapshot
Molecular Dynamics Characterization of Five Pathogenic Factor X Mutants Associated with Decreased Catalytic Activity
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inferred← citeshttps://doi.org/10.1093/bioadv/vbab042openalex-snapshot
A random forest classifier for protein–protein docking models
inferred← citeshttps://doi.org/10.1093/bioadv/vbad012openalex-snapshot
Improving classification of correct and incorrect protein–protein docking models by augmenting the training set
inferred← citeshttps://doi.org/10.1093/bioinformatics/btaf606openalex-snapshot
COCOMAPS 2.0: a web server for identifying, analyzing, and visualizing atomic interactions at the interface of biomolecular complexes
inferred← citeshttps://doi.org/10.1093/bioinformatics/btu837openalex-snapshot
CONSRANK: a server for the analysis, comparison and ranking of docking models based on inter-residue contacts
inferred← citeshttps://doi.org/10.1111/febs.12771openalex-snapshot
Integrative computational modeling of protein interactions
inferred← citeshttps://doi.org/10.1186/1471-2105-15-s5-s1openalex-snapshot
MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories
inferred← citeshttps://doi.org/10.1186/s12859-018-2414-9openalex-snapshot
Distinguishing crystallographic from biological interfaces in protein complexes: role of intermolecular contacts and energetics for classification
inferred← citeshttps://doi.org/10.1186/s12859-020-03600-8openalex-snapshot
The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses
inferred← citeshttps://doi.org/10.1186/s43088-022-00285-1openalex-snapshot
Computer-aided molecular modeling and structural analysis of the human centromere protein–HIKM complex
inferred← citeshttps://doi.org/10.1371/journal.pone.0102839openalex-snapshot
Structural Basis for the Recognition in an Idiotype-Anti-Idiotype Antibody Complex Related to Celiac Disease
inferred← citeshttps://doi.org/10.1371/journal.pone.0166460openalex-snapshot
Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models
inferred← citeshttps://doi.org/10.22541/au.162693577.78775249/v1openalex-snapshot
Computer-aided molecular modeling and structural analysis of the human centromere protein-HIKM complex
inferred← citeshttps://doi.org/10.3389/fmolb.2020.559005openalex-snapshot
Evaluation of CONSRANK-Like Scoring Functions for Rescoring Ensembles of Protein–Protein Docking Poses
inferred← citeshttps://doi.org/10.3390/biomedicines9121763openalex-snapshot
A Combined Spectroscopic and In Silico Approach to Evaluate the Interaction of Human Frataxin with Mitochondrial Superoxide Dismutase
inferred← citeshttps://doi.org/10.3390/molecules200712045openalex-snapshot
Analysis and Ranking of Protein-Protein Docking Models Using Inter-Residue Contacts and Inter-Molecular Contact Maps
inferred← citeshttps://doi.org/10.3390/molecules26092622openalex-snapshot
D936Y and Other Mutations in the Fusion Core of the SARS-CoV-2 Spike Protein Heptad Repeat 1: Frequency, Geographical Distribution, and Structural Effect
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Immunoinformatics-Aided Design of a Peptide Based Multiepitope Vaccine Targeting Glycoproteins and Membrane Proteins against Monkeypox Virus
inferred← citeshttps://doi.org/10.6084/m9.figshare.12965820openalex-snapshot
Additional file 1 of The CASP13-CAPRI targets as case studies to illustrate a novel scoring pipeline integrating CONSRANK with clustering and interface analyses
inferred← citeshttps://doi.org/10.6084/m9.figshare.20521602openalex-snapshot
Additional file 1 of Computer-aided molecular modeling and structural analysis of the human centromere protein–HIKM complex
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