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Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDock

https://doi.org/10.1002/prot.25851
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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/bip.360221211openalex-snapshot
Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
inferredcites →https://doi.org/10.1002/jcc.21287openalex-snapshot
CHARMM: The biomolecular simulation program
inferredcites →https://doi.org/10.1002/prot.10389openalex-snapshot
ZDOCK: An initial‐stage protein‐docking algorithm
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.20019openalex-snapshot
A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding
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.21419openalex-snapshot
pyDock: Electrostatics and desolvation for effective scoring of rigid‐body protein–protein docking
inferredcites →https://doi.org/10.1002/prot.21579openalex-snapshot
Energy minimization in low‐frequency normal modes to efficiently allow for global flexibility during systematic protein–protein docking
inferredcites →https://doi.org/10.1002/prot.21698openalex-snapshot
Implicit flexibility in protein docking: Cross‐docking and local refinement
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.24115openalex-snapshot
Flexible protein docking refinement using pose‐dependent normal mode analysis
inferredcites →https://doi.org/10.1002/prot.25215openalex-snapshot
Modeling protein–protein and protein–peptide complexes: CAPRI 6th edition
inferredcites →https://doi.org/10.1002/prot.25851openalex-snapshot
Enhanced sampling of protein conformational states for dynamic cross‐docking within the protein‐protein docking server SwarmDock
inferredcites →https://doi.org/10.1007/978-1-4939-0366-5_13openalex-snapshot
Predicting the Structure of Protein–Protein Complexes Using the SwarmDock Web Server
inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot
VMD: Visual molecular dynamics
inferredcites →https://doi.org/10.1016/j.jmb.2005.01.058openalex-snapshot
The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein–Protein Complexes with an Application to Protein–Protein Docking
inferredcites →https://doi.org/10.1016/j.jmb.2015.07.016openalex-snapshot
Updates to the Integrated Protein–Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2
inferredcites →https://doi.org/10.1016/j.str.2004.09.014openalex-snapshot
Complementarity of Structure Ensembles in Protein-Protein Binding
inferredcites →https://doi.org/10.1016/j.str.2016.06.025openalex-snapshot
Pushing the Backbone in Protein-Protein Docking
inferredcites →https://doi.org/10.1016/j.tibs.2010.04.009openalex-snapshot
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
inferredcites →https://doi.org/10.1021/acs.jctc.7b00197openalex-snapshot
NOLB: Nonlinear Rigid Block Normal-Mode Analysis Method
inferredcites →https://doi.org/10.1021/ja026939xopenalex-snapshot
HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information
inferredcites →https://doi.org/10.1038/nprot.2016.169openalex-snapshot
The ClusPro web server for protein–protein docking
inferredcites →https://doi.org/10.1074/mcp.m100026-mcp200openalex-snapshot
Describing Biological Protein Interactions in Terms of Protein States and State Transitions
inferredcites →https://doi.org/10.1093/bioinformatics/btt038openalex-snapshot
SwarmDock: a server for flexible protein–protein docking
inferredcites →https://doi.org/10.1093/bioinformatics/btv252openalex-snapshot
cNMA: a framework of encounter complex-based normal mode analysis to model conformational changes in protein interactions
inferredcites →https://doi.org/10.1093/nar/gkh368openalex-snapshot
ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
inferredcites →https://doi.org/10.1109/icnn.1995.488968openalex-snapshot
Particle swarm optimization
inferredcites →https://doi.org/10.1110/ps.0217002openalex-snapshot
Distance‐scaled, finite ideal‐gas reference state improves structure‐derived potentials of mean force for structure selection and stability prediction
inferredcites →https://doi.org/10.12688/f1000research.7931.1openalex-snapshot
FreeSASA: An open source C library for solvent accessible surface area calculations
inferredcites →https://doi.org/10.1287/moor.6.1.19openalex-snapshot
Minimization by Random Search Techniques
inferredcites →https://doi.org/10.1371/journal.pcbi.1005290openalex-snapshot
Computing the Dynamic Supramolecular Structural Proteome
inferredcites →https://doi.org/10.15252/embj.201798665openalex-snapshot
Helicobacter pylori adhesin HopQ disrupts trans dimerization in human CEACAMs
inferredcites →https://doi.org/10.3390/ijms11103623openalex-snapshot
SwarmDock and the Use of Normal Modes in Protein-Protein Docking

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inferred← citeshttps://doi.org/10.1016/j.drudis.2025.104382openalex-snapshot
Computational methods for modeling protein–protein interactions in the AI era: Current status and future directions
inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2021.06.200openalex-snapshot
The milk-derived lactoferrin inhibits V-ATPase activity by targeting its V1 domain
inferred← citeshttps://doi.org/10.1016/j.jmb.2022.167820openalex-snapshot
Domain-Based Protein Docking with Extremely Large Conformational Changes
inferred← citeshttps://doi.org/10.1016/j.sbi.2020.11.011openalex-snapshot
Advances to tackle backbone flexibility in protein docking
inferred← citeshttps://doi.org/10.1016/j.str.2022.09.005openalex-snapshot
A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility
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.1c01255openalex-snapshot
Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein–Protein Complexes
inferred← citeshttps://doi.org/10.1021/acs.jctc.4c00754openalex-snapshot
Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution
inferred← citeshttps://doi.org/10.1038/s41467-024-52119-6openalex-snapshot
Orientia tsutsugamushi Ank5 promotes NLRC5 cytoplasmic retention and degradation to inhibit MHC class I expression
inferred← citeshttps://doi.org/10.1039/9781788016544-00087openalex-snapshot
Computational Structural Modeling to Discover PPI Modulators
inferred← citeshttps://doi.org/10.1055/a-1967-2004openalex-snapshot
Effect Produced by a Cyclooctyne Derivative on Both Infarct Area and Left Ventricular Pressure via Calcium Channel Activation
inferred← citeshttps://doi.org/10.1101/2021.02.22.432196openalex-snapshot
Protein-protein docking with large-scale backbone flexibility using coarse-grained Monte-Carlo simulations
inferred← citeshttps://doi.org/10.1101/2023.12.04.569938openalex-snapshot
Orientia tsutsugamushi Ank5 directs ubiquitination and proteasomal degradation of NLRC5 to inhibit major histocompatibility complex class I expression
inferred← citeshttps://doi.org/10.14295/bjs.v3i1.455openalex-snapshot
Interaction of benzenesulfonamide derivatives with Smyd3 using a theoretical model
inferred← citeshttps://doi.org/10.33263/briac133.227openalex-snapshot
Efficient Synthesis of Two Chloramphenicol Derivatives as Antibacterial Agents
inferred← citeshttps://doi.org/10.3390/ijms22147341openalex-snapshot
Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations
inferred← citeshttps://doi.org/10.3390/molecules27061841openalex-snapshot
Modeling the Dynamics of Protein–Protein Interfaces, How and Why?
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