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A machine learning approach for ranking clusters of docked protein‐protein complexes by pairwise cluster comparison

https://doi.org/10.1002/prot.25218
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What this work says

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

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Peptide Folding: When Simulation Meets Experiment
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PROCOS: Computational analysis of protein–protein complexes
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On the analysis of protein–protein interactions via knowledge‐based potentials for the prediction of protein–protein docking
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ZDOCK: An initial‐stage protein‐docking algorithm
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Assessment of blind predictions of protein–protein interactions: Current status of docking methods
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A physical reference state unifies the structure‐derived potential of mean force for protein folding and binding
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Optimal docking area: A new method for predicting protein–protein interaction sites
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.20859openalex-snapshot
Optimal design of protein docking potentials: Efficiency and limitations
inferredcites →https://doi.org/10.1002/prot.21117openalex-snapshot
PIPER: An FFT‐based protein docking program with pairwise potentials
inferredcites →https://doi.org/10.1002/prot.21391openalex-snapshot
Flexible relaxation of rigid‐body docking solutions
inferredcites →https://doi.org/10.1002/prot.21495openalex-snapshot
FireDock: Fast interaction refinement in molecular docking
inferredcites →https://doi.org/10.1002/prot.22488openalex-snapshot
Improved prediction of protein side‐chain conformations with SCWRL4
inferredcites →https://doi.org/10.1002/prot.22550openalex-snapshot
PIE—Efficient filters and coarse grained potentials for unbound protein–protein docking
inferredcites →https://doi.org/10.1002/prot.24214openalex-snapshot
Improving ranking of models for protein complexes with side chain modeling and atomic potentials
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/10.1002/prot.24343openalex-snapshot
Sampling and scoring: A marriage made in heaven
inferredcites →https://doi.org/10.1002/prot.24366openalex-snapshot
Using the concept of transient complex for affinity predictions in CAPRI rounds 20–27 and beyond
inferredcites →https://doi.org/10.1002/prot.24428openalex-snapshot
Docking, scoring, and affinity prediction in CAPRI
inferredcites →https://doi.org/10.1002/prot.24678openalex-snapshot
Score_set: A CAPRI benchmark for scoring protein complexes
inferredcites →https://doi.org/10.1002/prot.24761openalex-snapshot
Inferring the microscopic surface energy of protein–protein interfaces from mutation data
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Extremely randomized trees
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Empirical characterization of random forest variable importance measures
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Computational prediction of protein interfaces: A review of data driven methods
inferredcites →https://doi.org/10.1016/j.sbi.2015.08.001openalex-snapshot
High-resolution protein–protein docking by global optimization: recent advances and future challenges
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Structure of the Yeast tRNA m7G Methylation Complex
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/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)00610-7openalex-snapshot
Insights into Protein–Protein Binding by Binding Free Energy Calculation and Free Energy Decomposition for the Ras–Raf and Ras–RalGDS Complexes
inferredcites →https://doi.org/10.1016/s0092-8674(00)80922-8openalex-snapshot
The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists
inferredcites →https://doi.org/10.1021/ci100353eopenalex-snapshot
Scoring by Intermolecular Pairwise Propensities of Exposed Residues (SIPPER): A New Efficient Potential for Protein−Protein Docking
inferredcites →https://doi.org/10.1021/ct400273topenalex-snapshot
Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
inferredcites →https://doi.org/10.1023/a:1010933404324openalex-snapshot
Random Forests
inferredcites →https://doi.org/10.1038/nmeth.2289openalex-snapshot
Interactome3D: adding structural details to protein networks
inferredcites →https://doi.org/10.1039/c005060copenalex-snapshot
Protein–protein docking tested in blind predictions: the CAPRI experiment
inferredcites →https://doi.org/10.1073/pnas.93.1.13openalex-snapshot
Principles of protein-protein interactions.
inferredcites →https://doi.org/10.1093/bioinformatics/btr513openalex-snapshot
Protein–protein binding affinity prediction on a diverse set of structures
inferredcites →https://doi.org/10.1093/bioinformatics/btt038openalex-snapshot
SwarmDock: a server for flexible protein–protein docking
inferredcites →https://doi.org/10.1093/bioinformatics/btt055openalex-snapshot
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
inferredcites →https://doi.org/10.1093/bioinformatics/btu097openalex-snapshot
ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers
inferredcites →https://doi.org/10.1093/bioinformatics/btu594openalex-snapshot
CCharPPI web server: computational characterization of protein–protein interactions from structure
inferredcites →https://doi.org/10.1093/bioinformatics/btw514openalex-snapshot
PRODIGY: a web server for predicting the binding affinity of protein–protein complexes
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Clustering Using a Similarity Measure Based on Shared Near Neighbors
inferredcites →https://doi.org/10.1177/001316445701700204openalex-snapshot
Elementary Linkage Analysis for Isolating Orthogonal and Oblique Types and Typal Relevancies
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/10.1186/1472-6807-10-40openalex-snapshot
Designing coarse grained-and atom based-potentials for protein-protein docking
inferredcites →https://doi.org/10.1186/1472-6807-10-s1-s3openalex-snapshot
Generalized spring tensor models for protein fluctuation dynamics and conformation changes
inferredcites →https://doi.org/10.1371/journal.pcbi.1002351openalex-snapshot
Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding
inferredcites →https://doi.org/10.1371/journal.pcbi.1002623openalex-snapshot
Alternative Protein-Protein Interfaces Are Frequent Exceptions
inferredcites →https://doi.org/10.1371/journal.pcbi.1003216openalex-snapshot
Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization
inferredcites →https://doi.org/10.1371/journal.pone.0015386openalex-snapshot
A Novel Side-Chain Orientation Dependent Potential Derived from Random-Walk Reference State for Protein Fold Selection and Structure Prediction
inferredcites →https://doi.org/10.3390/ijms11103623openalex-snapshot
SwarmDock and the Use of Normal Modes in Protein-Protein Docking
inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot
Scikit-learn: Machine Learning in Python
inferredcites →https://doi.org/10.7554/elife.07454openalex-snapshot
Contacts-based prediction of binding affinity in protein–protein complexes

What points at this work

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

inferred← citeshttps://doi.org/10.1002/prot.25612openalex-snapshot
Refinement of protein‐protein complexes in contact map space with metadynamics simulations
inferred← citeshttps://doi.org/10.1002/prot.25973openalex-snapshot
Refinement of pairwise potentials via logistic regression to score protein‐protein interactions
inferred← citeshttps://doi.org/10.1007/978-1-0716-0708-4_11openalex-snapshot
A Guide for Protein–Protein Docking Using SwarmDock
inferred← citeshttps://doi.org/10.1007/978-1-4939-7759-8_27openalex-snapshot
Flexible Protein-Protein Docking with SwarmDock
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.04.028openalex-snapshot
Improved cluster ranking in protein–protein docking using a regression approach
inferred← citeshttps://doi.org/10.1016/j.ijcce.2020.04.001openalex-snapshot
Mapping ontology vertices to a line using hypergraph framework
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00687openalex-snapshot
GroScore: Accurate Scoring of Protein–Protein Binding Poses Using Explicit-Solvent Free-Energy Calculations
inferred← citeshttps://doi.org/10.1021/acs.jctc.1c00336openalex-snapshot
Native or Non-Native Protein–Protein Docking Models? Molecular Dynamics to the Rescue
inferred← citeshttps://doi.org/10.1038/s41598-017-00266-wopenalex-snapshot
Disentangling constraints using viability evolution principles in integrative modeling of macromolecular assemblies
inferred← citeshttps://doi.org/10.1038/s41598-018-23982-3openalex-snapshot
Protein docking refinement by convex underestimation in the low-dimensional subspace of encounter complexes
inferred← citeshttps://doi.org/10.1080/08927022.2024.2378833openalex-snapshot
Modified heated CGMD simulations for discovering stable docked conformations of BiTE antibody against CD3 and CD117/c-kit
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty635openalex-snapshot
SKEMPI 2.0: an updated benchmark of changes in protein–protein binding energy, kinetics and thermodynamics upon mutation
inferred← citeshttps://doi.org/10.1142/s021819401930001xopenalex-snapshot
Machine Learning Methods for Ranking
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Predicting improved protein conformations with a temporal deep recurrent neural network
inferred← citeshttps://doi.org/10.2174/1386207323999200918151331openalex-snapshot
In-silico Studies and Biological Activity of Potential BACE-1 Inhibitors
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RETRACTED: Research on fuzzy English automatic recognition and human-computer interaction based on machine learning
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