ArticleNature communications2022
Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
46 citing papers in PubMed, 122 citations in OpenAlex.
- Molecular Dynamics Simulations Reveal Structural Changes Associated with the ABCA1 R230C Functional Variant.International journal of molecular sciences · 2026Article
- Targeting BCL-2 through Deep Learning-Based Drug Repurposing: A Multimodal Approach Combining Diffusion-Based Generative Modeling, Neural Relational Inference, and In Vitro Validation.Journal of chemical information and modeling · 2026Article
- AlloPool is a deep learning framework that infers protein allostery from molecular dynamics simulations.PLoS biology · 2026Article
- Agonist Binding Reshapes the Kinetic Landscape and Allosteric Communication of APLNR Toward Activation-Competent States.International journal of molecular sciences · 2026Article
- Accurate and Time-Efficient Condensed-Phase Free Energy Simulations with Reaction Specific Δ-Machine Learning Potentials in CHARMM.Journal of chemical theory and computation · 2026Article
- Temperature-Dependent Reorganization of Conformational Dynamics and Interaction Networks Underlies Thermostability in PET-Degrading Enzymes.International journal of molecular sciences · 2026Article
- Artificial Intelligence and Protein Design: A retrospective study on 20-year emerging trends and core research areas from bibliometric perspectives.Probiotics and antimicrobial proteins · 2026Article
- Artificial intelligence in the assessment of epilepsy-related genetic mutations: Learned from GABAEpilepsia open · 2026Review
- Targeting frizzled receptors (FZDs) for anti-tumor therapy: From orthosteric to allosteric inhibition.Acta pharmaceutica Sinica. B · 2026Review
- Computational Identification of Potential Novel Allosteric IHF Inhibitors Using QSAR Modeling to Inhibit Plasmid-Mediated Antibiotic Resistance.International journal of molecular sciences · 2026Article
- Carba-NAD binding activates SIR2 by reshaping conformational plasticity and rewiring long-range allosteric networks.PLoS computational biology · 2026Article
- Steric confinement-induced emission probe for monitoring protein conformations in live cells.Communications chemistry · 2026Article
- Mutation-Induced Resistance of SARS-CoV-2 MInternational journal of molecular sciences · 2026Article
- Network reorganization of a cold-adapted β-glucosidase couples conformational flexibility to catalytic efficiency under low-temperature conditions.Frontiers in microbiology · 2026Article
- Allosteric Activation through Coordinated Energy Landscape Reweighting and Information Flow.Computational and structural biotechnology journal · 2026Article
- Article
- The Evolving Landscape of Protein Allostery: From Computational and Experimental Perspectives.Journal of molecular biology · 2025Review
- Mamba time series forecasting with uncertainty quantification.Machine learning: science and technology · 2025Article
- Exploring the toxicological effects of DOTP exposure on periodontitis by combining molecular docking and molecular dynamics simulations.Scientific reports · 2025Article
- Conformational Remodeling and Allosteric Regulation Underlying EGFR Mutant-Induced Activation: A Multi-Scale Analysis Using MD, MSMs, and NRI.International journal of molecular sciences · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
Abstract
Protein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid change at a distant site affects the active site remotely. Molecular dynamics (MD) simulation provides a powerful computational approach to probe the allosteric effect. However, current MD simulations cannot reach the time scales of whole allosteric processes. The advent of deep learning made it possible to evaluate both spatially short and long-range communications for understanding allostery. For this purpose, we applied a neural relational inference model based on a graph neural network, which adopts an encoder-decoder architecture to simultaneously infer latent interactions for probing protein allosteric processes as dynamic networks of interacting residues. From the MD trajectories, this model successfully learned the long-range interactions and pathways that can mediate the allosteric communications between distant sites in the Pin1, SOD1, and MEK1 systems. Furthermore, the model can discover allostery-related interactions earlier in the MD simulation trajectories and predict relative free energy changes upon mutations more accurately than other methods.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.