Softwares developed in the Noskov lab including BROMOC and QM/MM FEP can be used to tackle projects on effective potential, polymers dynamics in nanopores, voltage-gated ion channel kinetics.
Polymer Dynamics in nanopores
BROMOC: Grand-Canonical Monte-Carlo/Brownian Dynamics for studies of polymer transport in nanopores
BROMOC 4.03 : Source code + Documentation
GCMC/BD was originally developed in the Benoit Roux Lab by Wonpil Im and Benoit Roux. A program suite now include capabilities for analysis (distribution function, time-correlation series), force-field development (reverse Monte-Carlo) as well as opportunity to study ss-DNA dynamics in the nanopore. The version of the code along with a manual can be found here. Please feel free to send us both positive and negative comments for they truly help improving our code.
How to use BROMOC : Tutorial
Effective Potentials
How to compute your own EP and ECP : Tutorial
Precomputed EP/ECP for DNA-KCl
Description to be added
If you use BROMOC or our EP/ECP please cite us:
BROMOC-D: Brownian Dynamics/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores
Pablo M. De Biase, Carlos J. F. Solano, Suren Markosyan, Luke Czapla, and Sergei Yu. Noskov*
J Chem Theory Comput. Jul 10, 2012; 8(7): 2540-2551.
Published online 24 May 2012
DOI: 10.1021/ct3004244
Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials
Pablo M. De Biase*, Suren Markosyan and Sergei Noskov*
J Comput Chem. 2014 Apr 5;35(9):711-721.
Published online: 12 FEB 2014
DOI: 10.1002/jcc.23544
VGC-KiMo: Voltage-Gated Ion Channels Kinetic Modeling for Whole-Cell Voltage-Clamp Recordings
VGC-KiMo software allows for kinetic modeling of voltage-gated ion channels using whole cell voltage-clamp data. Sets of data from various experimental voltage protocols are analyzed simultaneously and fitted to Markov chain models. The minimization procedure allows to assess the right model and the corresponding kinetic parameters that describe the channel kinetics. In the current form, the source code includes a Markov formulation for the Kv11.1 or hERG K+ channel. Any other ion channel could be added to the source code in addition to the current one, different Markov models and other voltage protocols.
If you use VGC-KiMo please cite us:
Kinetic model for NS1643 drug activation of WT and L529I variants of Kv11. 1 (hERG1) potassium channel.
Perissinotti, L.L., Guo, J., De Biase, P.M., Clancy, C.E., Duff, H.J. and Noskov, S.Y.*
Biophysical journal 2015 Mar 24; 08(6), pp.1414-1424.
DOI: 10.1016/j.bpj.2014.12.056
Determinants of isoform-specific gating kinetics of hERG1 channel: combined experimental and simulation study.
Perissinotti, L.L., De Biase, P.M., Guo, J., Yang, P.C., Lee, M.C., Clancy, C.E., Duff, H.J. and Noskov, S.Y.*
Frontiers in physiology 2018 Apr 12;9:207.
DOI: 10.3389/fphys.2018.00207
QM/MM FEP
Examples for CHARMM/deMon2k, Prompts for download and install
