{"id":186,"date":"2020-02-07T22:07:27","date_gmt":"2020-02-08T04:07:27","guid":{"rendered":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/?page_id=186"},"modified":"2020-04-17T11:39:32","modified_gmt":"2020-04-17T17:39:32","slug":"softwares-developed","status":"publish","type":"page","link":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/softwares-developed\/","title":{"rendered":"Softwares Developed"},"content":{"rendered":"\n

Softwares developed in the Noskov lab<\/strong> including BROMOC and QM\/MM FEP can be used to tackle projects on effective potential, polymers dynamics in nanopores, voltage-gated ion channel kinetics.<\/p>\n\n\n\n

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Polymer Dynamics in nanopores<\/h2>\n\n\n\n

BROMOC: Grand-Canonical Monte-Carlo\/Brownian Dynamics for studies of polymer transport in nanopores<\/h4>\n\n\n\n

BROMOC 4.03 : Source code + Documentation<\/a><\/p>\n\n\n\n

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.<\/p>\n\n\n\n

How to use BROMOC :  Tutorial<\/a><\/p>\n\n\n\n

Effective Potentials<\/h4>\n\n\n\n

How to compute your own EP and ECP : Tutorial<\/a><\/p>\n\n\n\n

Precomputed\u00a0EP\/ECP<\/a>\u00a0for DNA-KCl<\/p>\n\n\n\n

Description to be added<\/p>\n\n\n\n   \n\n\n

If you use BROMOC or our EP\/ECP please cite us:<\/em><\/p>\n\n\n

BROMOC-D: Brownian Dynamics\/Monte-Carlo Program Suite to Study Ion and DNA Permeation in Nanopores<\/strong>
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<\/p>\n\n\n\n

Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials<\/strong>
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<\/p>\n\n\n\n

VGC-KiMo: Voltage-Gated Ion Channels Kinetic Modeling for Whole-Cell Voltage-Clamp Recordings<\/h2>\n\n\n\n

Source code<\/a><\/p>\n\n\n\n

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.<\/p>\n\n\n\n   \n\n\n

If you use VGC-KiMo please cite us:<\/em><\/p>\n\n\n

Kinetic model for NS1643 drug activation of WT and L529I variants of Kv11. 1 (hERG1) potassium channel<\/strong>.
Perissinotti, L.L., Guo, J., De Biase, P.M., Clancy, C.E., Duff, H.J. and Noskov, S.Y.*
Biophysical journal<\/em> \u00a02015 Mar 24; 08<\/em>(6), pp.1414-1424.
DOI: 10.1016\/j.bpj.2014.12.056 <\/p>\n\n\n\n

Determinants of isoform-specific gating kinetics of hERG1 channel: combined experimental and simulation study<\/strong>.
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<\/em> 2018 Apr 12;9:207<\/em>.
DOI: 10.3389\/fphys.2018.00207<\/p>\n\n\n\n

QM\/MM FEP<\/h2>\n\n\n\n

Examples for CHARMM\/deMon2k, Prompts for download and install<\/p>\n\n\n\n

<\/p>\n","protected":false},"excerpt":{"rendered":"

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 …<\/p>\n","protected":false},"author":66,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"ngg_post_thumbnail":0,"footnotes":""},"class_list":["post-186","page","type-page","status-publish","hentry"],"featured_image_src":null,"featured_image_src_square":null,"_links":{"self":[{"href":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/wp-json\/wp\/v2\/pages\/186","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/wp-json\/wp\/v2\/users\/66"}],"replies":[{"embeddable":true,"href":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/wp-json\/wp\/v2\/comments?post=186"}],"version-history":[{"count":14,"href":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/wp-json\/wp\/v2\/pages\/186\/revisions"}],"predecessor-version":[{"id":463,"href":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/wp-json\/wp\/v2\/pages\/186\/revisions\/463"}],"wp:attachment":[{"href":"https:\/\/wpsites.ucalgary.ca\/noskovlab\/wp-json\/wp\/v2\/media?parent=186"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}