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Improved flexible refinement of protein docking in CAPRI rounds 22–27

https://doi.org/10.1002/prot.24404
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What this work says

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

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Effective energy function for proteins in solution
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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
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Validation of the general purpose QUANTA ®3.2/CHARMm® force field
inferredcites →https://doi.org/10.1002/prot.10381openalex-snapshot
CAPRI: A Critical Assessment of PRedicted Interactions
inferredcites →https://doi.org/10.1002/prot.20551openalex-snapshot
Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures
inferredcites →https://doi.org/10.1002/prot.21754openalex-snapshot
Docking with PIPER and refinement with SDU in rounds 6–11 of CAPRI
inferredcites →https://doi.org/10.1002/prot.21795openalex-snapshot
ClusPro: Performance in CAPRI rounds 6–11 and the new server
inferredcites →https://doi.org/10.1002/prot.21804openalex-snapshot
Docking and scoring protein complexes: CAPRI 3rd Edition
inferredcites →https://doi.org/10.1002/prot.22668openalex-snapshot
FiberDock: Flexible induced‐fit backbone refinement in molecular docking
inferredcites →https://doi.org/10.1002/prot.22818openalex-snapshot
Docking and scoring protein interactions: CAPRI 2009
inferredcites →https://doi.org/10.1002/prot.22835openalex-snapshot
Achieving reliability and high accuracy in automated protein docking: Cluspro, PIPER, SDU, and stability analysis in CAPRI rounds 13–19
inferredcites →https://doi.org/10.1002/prot.23177openalex-snapshot
Assessment of template based protein structure predictions in CASP9
inferredcites →https://doi.org/10.1016/0022-2836(78)90302-9openalex-snapshot
Computer analysis of protein-protein interaction
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Structure of the Ultra-High-Affinity Colicin E2 DNase–Im2 Complex
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Putting an N-terminal end to the Clostridium thermocellum xylanase Xyn10B story: Crystal structure of the CBM22-1–GH10 modules complexed with xylohexaose
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/j.str.2011.04.006openalex-snapshot
Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination
inferredcites →https://doi.org/10.1016/s0959-440x(02)00285-3openalex-snapshot
Prediction of protein–protein interactions by docking methods
inferredcites →https://doi.org/10.1021/ct200931copenalex-snapshot
Charge Optimization Theory for Induced-Fit Ligands
inferredcites →https://doi.org/10.1021/j100058a043openalex-snapshot
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1021/jp973084fopenalex-snapshot
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
inferredcites →https://doi.org/10.1073/pnas.0802496105openalex-snapshot
Insights into protein flexibility: The relationship between normal modes and conformational change upon protein–protein docking
inferredcites →https://doi.org/10.1073/pnas.0904214106openalex-snapshot
The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding
inferredcites →https://doi.org/10.1093/bioinformatics/btr168openalex-snapshot
ProDy : Protein Dynamics Inferred from Theory and Experiments
inferredcites →https://doi.org/10.1093/nar/gkg543openalex-snapshot
Tools for comparative protein structure modeling and analysis
inferredcites →https://doi.org/10.1093/nar/gkh468openalex-snapshot
Protein structure prediction and analysis using the Robetta server
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/10.1109/tac.2007.894518openalex-snapshot
SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking
inferredcites →https://doi.org/10.1110/ps.40001openalex-snapshot
Optimization of binding electrostatics: Charge complementarity in the barnase‐barstar protein complex
inferredcites →https://doi.org/10.1126/science.1202617openalex-snapshot
Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin
inferredcites →https://doi.org/10.1186/1471-2105-9-40openalex-snapshot
I-TASSER server for protein 3D structure prediction
inferredcites →https://doi.org/10.1371/journal.pcbi.1000191openalex-snapshot
Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes
inferredcites →https://doi.org/10.1529/biophysj.105.070045openalex-snapshot
Can Conformational Change Be Described by Only a Few Normal Modes?
inferredcites →https://doi.org/10.3390/ijms11103623openalex-snapshot
SwarmDock and the Use of Normal Modes in Protein-Protein Docking

What points at this work

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

inferred← citeshttps://doi.org/10.1002/humu.23826openalex-snapshot
Predicting pathogenicity of missense variants with weakly supervised regression
inferred← citeshttps://doi.org/10.1002/prot.25212openalex-snapshot
Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility
inferred← citeshttps://doi.org/10.1002/prot.25234openalex-snapshot
Addressing recent docking challenges: A hybrid strategy to integrate template‐based and free protein‐protein docking
inferred← citeshttps://doi.org/10.1007/s44372-025-00460-5openalex-snapshot
Nanopore sequencing for molecular diagnostics of plant pathogens and environmental monitoring to enhance crop health and sustainability
inferred← citeshttps://doi.org/10.1016/j.drudis.2014.02.005openalex-snapshot
Search strategies and evaluation in protein–protein docking: principles, advances and challenges
inferred← citeshttps://doi.org/10.1016/j.drudis.2015.03.007openalex-snapshot
Exploring the potential of global protein–protein docking: an overview and critical assessment of current programs for automatic ab initio docking
inferred← citeshttps://doi.org/10.1016/j.sbi.2015.08.001openalex-snapshot
High-resolution protein–protein docking by global optimization: recent advances and future challenges
inferred← citeshttps://doi.org/10.1016/j.str.2016.06.025openalex-snapshot
Pushing the Backbone in Protein-Protein Docking
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c01029openalex-snapshot
Exploring Protein–Protein Docking Tools: Comprehensive Insights into Traditional and Deep-Learning Approaches
inferred← citeshttps://doi.org/10.1021/acs.jctc.0c00476openalex-snapshot
Bayesian Active Learning for Optimization and Uncertainty Quantification in Protein Docking
inferred← citeshttps://doi.org/10.1021/acs.jctc.6b01110openalex-snapshot
Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method
inferred← citeshttps://doi.org/10.1038/nprot.2016.169openalex-snapshot
The ClusPro web server for protein–protein docking
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty564openalex-snapshot
iCFN: an efficient exact algorithm for multistate protein design
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Determination of an effective scoring function for RNA–RNA interactions with a physics-based double-iterative method
inferred← citeshttps://doi.org/10.1109/bibm.2013.6732462openalex-snapshot
Using evolutionary couplings to optimize dimer prediction with Rosetta SymDock
inferred← citeshttps://doi.org/10.1246/bcsj.20220239openalex-snapshot
Molecular Dynamics Simulation of the Antigen–Antibody Complex Formation Process between Hen Egg-White Lysozyme and HyHEL-10
inferred← citeshttps://doi.org/10.4155/fmc-2017-0261openalex-snapshot
Development of a New Benchmark for Assessing the Scoring Functions Applicable to Protein–Protein Interactions
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