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Unsupervised Graph-Based Learning Predicts Mutations That Alter Protein Dynamics

https://doi.org/10.1101/847426
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
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Specific Labeling of Polypeptides at Amino-Terminal Cysteine Residues Using Cy5-benzyl Thioester
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Ratiometric Analysis of Single-Molecule Fluorescence Resonance Energy Transfer Using Logical Combinations of Threshold Criteria: A Study of 12-mer DNA
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A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
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Prediction of allosteric sites and mediating interactions through bond-to-bond propensities
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The energy landscape of adenylate kinase during catalysis
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Data-driven unsupervised clustering of online learner behaviour
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Molecular dynamics and protein function
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Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
inferredcites →https://doi.org/10.1073/pnas.0902159106openalex-snapshot
Protein elastic network models and the ranges of cooperativity
inferredcites →https://doi.org/10.1073/pnas.0903215107openalex-snapshot
Stability of graph communities across time scales
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Structural basis for ligand binding to an enzyme by a conformational selection pathway
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Protein multi-scale organization through graph partitioning and robustness analysis: application to the myosin–myosin light chain interaction
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Fast unfolding of communities in large networks
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Proteins across scales through graph partitioning: application to the major peanut allergen Ara h 1
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The Protein Data Bank
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Chemistry across scales: from molecules to cells
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Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins
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Random Walks, Markov Processes and the Multiscale Modular Organization of Complex Networks
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Normal modes for predicting protein motions: A comprehensive database assessment and associated Web tool
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Graph centrality is a question of scale
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Flow-Based Network Analysis of the Caenorhabditis elegans Connectome
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The Role of Stochastic and Modal Gating of Cardiac L-Type Ca2+ Channels on Early After-Depolarizations
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Small- and Large-Scale Conformational Changes of Adenylate Kinase: A Molecular Dynamics Study of the Subdomain Motion and Mechanics
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Semi-supervised classification on graphs using explicit diffusion dynamics

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

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Algorithm 1044: PyGenStability, a Multiscale Community Detection Framework with Generalized Markov Stability
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