ArticleBiophysical journal2020
Exploring Conformational Change of Adenylate Kinase by Replica Exchange Molecular Dynamic Simulation.
Article in Biophysical journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Protein Structuromics Reveals a Loop-Controlled Half-Open Active Pocket Conformation Throughout Fe(II)/α-ketoglutarate-Dependent Dioxygenase Catalytic Cycle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Exploring the conformational landscape of adenylate kinase and beyond with protein folding models.Scientific reports · 2026Article
- MDGraphEmb: a toolkit for graph embedding and classification of protein conformational ensembles.Bioinformatics (Oxford, England) · 2025Article
- Novel AK-1 gene variants combined with thalassemia causing rare hereditary non-spherocytic hemolytic anemia in a Chinese family.Annals of hematology · 2025Article
- Toward the Prediction of Binding Events in Very Flexible, Allosteric, Multidomain Proteins.Journal of chemical information and modeling · 2025Article
- Predicting binding events in very flexible, allosteric, multi-domain proteins.bioRxiv : the preprint server for biology · 2024Article
- Structure-based drug design and molecular dynamics studies of an allosteric modulator targeting the protein-protein interaction site of PDK1.Journal of molecular modeling · 2024Article
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins.Journal of chemical information and modeling · 2023Article
- Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling.Quarterly reviews of biophysics · 2023Review
- Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase.The journal of physical chemistry. B · 2022Article
- Red cell adenylate kinase deficiency in China: molecular study of 2 new mutations (413G > A, 223dupA).BMC medical genomics · 2022Article
- Probing the competitive inhibitor efficacy of frog-skin alpha helical AMPs identified against ACE2 binding to SARS-CoV-2 S1 spike protein as therapeutic scaffold to prevent COVID-19.Journal of molecular modeling · 2022Article
- Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic.Computational biology and chemistry · 2021Review
- Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery.Computers in biology and medicine · 2021Review
- An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules.Journal of chemical theory and computation · 2020Article
- D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19.Acta pharmaceutica Sinica. B · 2020Article
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Replica exchange molecular dynamics (REMD) simulation is a popular enhanced sampling method that is widely used for exploring the atomic mechanism of protein conformational change. However, the requirement of huge computational resources for REMD, especially with the explicit solvent model, largely limits its application. In this study, the availability and efficiency of a variant of velocity-scaling REMD (vsREMD) was assessed with adenylate kinase as an example. Although vsREMD achieved results consistent with those from conventional REMD and experimental studies, the number of replicas required for vsREMD (30) was much less than that for conventional REMD (80) to achieve a similar acceptance rate (∼0.2), demonstrating high efficiency of vsREMD to characterize the protein conformational change and associated free-energy profile. Thus, vsREMD is a highly efficient approach for studying the large-scale conformational change of protein systems.
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