ArticleJournal of computational chemistry2012
Web interface for Brownian dynamics simulation of ion transport and its applications to beta-barrel pores.
Article in Journal of computational chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 48 citations in OpenAlex.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- A physical derivation of high-flux ion transport in biological channel via quantum ion coherence.Nature communications · 2024Article
- A Deep Dive into VDAC1 Conformational Diversity Using All-Atom Simulations Provides New Insights into the Structural Origin of the Closed States.International journal of molecular sciences · 2022Article
- The intrinsically disordered N-terminus of the voltage-dependent anion channel.PLoS computational biology · 2021Article
- Single-molecule sensing of peptides and nucleic acids by engineered aerolysin nanopores.Nature communications · 2019Article
- A Crucial Role for Side-Chain Conformation in the Versatile Charge Selectivity of Cys-Loop Receptors.Biophysical journal · 2019Article
- Effect of late endosomal DOBMP lipid and traditional model lipids of electrophysiology on the anthrax toxin channel activity.Biochimica et biophysica acta. Biomembranes · 2018Article
- Effect of endosomal acidification on small ion transport through the anthrax toxin PAFEBS letters · 2017Article
- CHARMM-GUI 10 years for biomolecular modeling and simulation.Journal of computational chemistry · 2017Review
- Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability.Biophysical journal · 2016Article
- Concerted motions networking pores and distant ferroxidase centers enable bacterioferritin function and iron traffic.Biochemistry · 2015Article
- Review
- Side-chain conformation at the selectivity filter shapes the permeation free-energy landscape of an ion channel.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Cationic PAMAM dendrimers as pore-blocking binary toxin inhibitors.Biomacromolecules · 2014Article
- Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials.Journal of computational chemistry · 2014Article
- Theoretical frameworks for multiscale modeling and simulation.Current opinion in structural biology · 2014Review
- CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.Advances in protein chemistry and structural biology · 2014Review
- Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations.The Journal of general physiology · 2013Article
- Theory of polymer-nanopore interactions refined using molecular dynamics simulations.Journal of the American Chemical Society · 2013Article
- Modeling and simulation of ion channels.Chemical reviews · 2012Review
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
Brownian dynamics (BD) based on accurate potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for carrying out grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), α-Hemolysin (α-HL), and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate the system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC, and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and α-HL, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10-20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5-7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement.
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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.