ArticleACS central science2017
Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis.
Article in ACS central science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Residue Interaction Network Reveals Allosteric Pathways Linking Orthosteric and Intracellular Sites in Class A GPCRs.Journal of chemical information and modeling · 2026Article
- Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1.Journal of chemical information and modeling · 2026Article
- Seq2Bind webserver for binding site prediction from sequences using fine-tuned protein language models.NAR genomics and bioinformatics · 2025Article
- Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases.Computational and structural biotechnology journal · 2025Article
- From complex data to clear insights: visualizing molecular dynamics trajectories.Frontiers in bioinformatics · 2024Review
- Article
- Molecular Dynamics and Machine Learning Give Insights on the Flexibility-Activity Relationships in Tyrosine Kinome.Journal of chemical information and modeling · 2023Article
- Combining structural and coevolution information to unveil allosteric sites.Chemical science · 2023Article
- GSK-3β Allosteric Inhibition: A Dead End or a New Pharmacological Frontier?International journal of molecular sciences · 2023Review
- Sparse group selection and analysis of function-related residue for protein-state recognition.Journal of computational chemistry · 2022Article
- Structure-based design of CDC42 effector interaction inhibitors for the treatment of cancer.Cell reports · 2022Article
- Computational drug discovery under RNA times.QRB discovery · 2022Review
- Probabilistic Pocket Druggability PredictionFrontiers in pharmacology · 2022Article
- Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface.The journal of physical chemistry letters · 2021Article
- Chemical Modulation of the 1-(Piperidin-4-yl)-1,3-dihydro-2Molecules (Basel, Switzerland) · 2021Article
- Finding Druggable Sites in Proteins Using TACTICS.Journal of chemical information and modeling · 2021Article
- Molecular Recognition by Gold Nanoparticle-Based Receptors as Defined through Surface Morphology and Pockets Fingerprint.The journal of physical chemistry letters · 2021Article
- Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations.The journal of physical chemistry letters · 2021Article
- Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors.International journal of molecular sciences · 2020Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The detection and characterization of binding pockets and allosteric communication in proteins is crucial for studying biological regulation and performing drug design. Nowadays, ever-longer molecular dynamics (MD) simulations are routinely used to investigate the spatiotemporal evolution of proteins. Yet, there is no computational tool that can automatically detect all the pockets and potential allosteric communication networks along these extended MD simulations. Here, we use a novel and fully automated algorithm that examines pocket formation, dynamics, and allosteric communication embedded in microsecond-long MD simulations of three pharmaceutically relevant proteins, namely, PNP, A2A, and Abl kinase. This dynamic analysis uses pocket crosstalk, defined as the temporal exchange of atoms between adjacent pockets, along the MD trajectories as a fingerprint of hidden allosteric communication networks. Importantly, this study indicates that dynamic pocket crosstalk analysis provides new mechanistic understandings on allosteric communication networks, enriching the available experimental data. Thus, our results suggest the prospective use of this unprecedented dynamic analysis to characterize transient binding pockets for structure-based drug design.
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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.