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Protocols

GCMC/BD specifications

Information


Unique identifier OMICS_13829
Name GCMC/BD
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Source code URL http://www.charmm-gui.org/download/gcmcbd.tar.gz
Maintained Yes

Publication for GCMC/BD

GCMC/BD citations

 (7)
library_books

Accessing gap junction channel structure function relationships through molecular modeling and simulations

2017
BMC Cell Biol
PMCID: 5267332
PMID: 28124624
DOI: 10.1186/s12860-016-0121-9

[…] sidue and the side-chain associated with residues K15, S17 and S19. In their first simulation, Kwon et al. [] used ion-flux calculations via grand-canonical monte-carlo brownian dynamics simulations (GCMC/BD) of this structure and showed that the pore region was too narrow to account for the experimentally observed currents. Under a transmembrane potential, these simulations predicted a marked inw […]

call_split

Magic Angle Spinning Nuclear Magnetic Resonance Characterization of Voltage Dependent Anion Channel Gating in Two Dimensional Lipid Crystalline Bilayers

2014
Biochemistry
PMCID: 4318587
PMID: 25545271
DOI: 10.1021/bi501260r
call_split See protocol

[…] Grand-Canonical Monte Carlo simulations utilizing an algorithm of Im, Seefeld, and Roux. The newly developed method of Luo et al. and Egwolf et al. was used to assess the reaction field component for GCMC/BD simulations. The details of Poisson–Boltzmann computations required for obtaining static and reaction field maps can be found in ref (). In all BROMOC simulations, the VDAC channel was treated […]

library_books

Voltage Regulation of Connexin Channel Conductance

2014
PMCID: 4276742
PMID: 25510741
DOI: 10.3349/ymj.2015.56.1.1

[…] t allow determination of functional properties of atomic structures. These are exemplified by, but not restricted to, determination of ion permeation through large pore ion channels by application of GCMC/BD,,,, calculation of gating charge, and calculation of free energy differences (ΔΔG) arising from mutation by FEP/MD. These methods provide a powerful mean to test the validity of atomic structu […]

library_books

Motifs in the permeation pathway of connexin channels mediate voltage and Ca2+ sensing

2014
Front Physiol
PMCID: 3978323
PMID: 24744733
DOI: 10.3389/fphys.2014.00113

[…] is not common in other channels.The relation between the published connexin crystal structure and the permeability properties were recently assessed by Grand Canonical Monte Carlo Brownian dynamics (GCMC/BD) (Kwon et al., ). To perform these calculations meaningfully, the missing regions and residues of the channel that were unresolved in the crystal structure were added and the structure minimiz […]

library_books

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations

2013
PMCID: 3787774
PMID: 24081985
DOI: 10.1085/jgp.201311014

[…] realistic implementation of asymmetric ion concentration and transmembrane potential boundary conditions, a grand canonical Monte Carlo (GCMC)/Brownian dynamics (BD) was implemented previously (). In GCMC/BD, asymmetric boundary conditions were imposed on a finite nonperiodic simulated system surrounded by concentration buffer regions (). Although this method provided important insight into the fa […]

library_books

BROMOC D: Brownian Dynamics/Monte Carlo Program Suite to Study Ion and DNA Permeation in Nanopores

2012
J Chem Theory Comput
PMCID: 3396124
PMID: 22798730
DOI: 10.1021/ct3004244

[…] Here, we present some computational illustrations of the developed framework for simulating DNA dynamics in nanopores. All GCMC/BD simulations were run on a single-core Xeon 2.4 GHz processor. The run-time for 1 μs of a GCMC/BD simulation for ss-poly(dA/C)25 blocking α-hemolysin ranges from 1 day in 300 mM KCl to 12 days […]

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GCMC/BD institution(s)
Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, KS, USA; Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA; Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
GCMC/BD funding source(s)
This work was supported in part by institutional funding from the University of Kansas General Research Fund allocation #2301388-003, Kansas-COBRE NIH P20 RR-17708, the National Science Foundation (NSF OCI-0503992) through TeraGrid resources provided by Purdue University, a research fellowship from the German Research Foundation, a NIH GM062342 grant, and the Intramural Research Program of the National Heart, Lung, and Blood Institute in the National Institutes of Health.

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