Sending report ...BioMOCA Suite
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Usage Stats Last 12 Months: Updated 16 May, 2008 more › Users: 40 Jobs: 338 Avg. exec. time: 60 secs Reviews & Citations Google/IEEE Avg. Review: Citations: 0
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Supporting Documents
- 1mag.pqr (PQR, 36.66 Kb)
- 2bg9_ph7.4_aligned.pqr (PQR, 2 Mb)
| Contributor(s) | David Papke, Reza Toghraee, Umberto Ravaioli University of Illinois, Urbana-Champaign |
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| At a glance | Simulates ion flow through a channel. |
| Description | The BioMOCA Suite can perform ion channel flow simulations on any user supplied channel. The suite includes: a map generator subtool, which produces protein maps for BioMOCA from the supplied PQR file; a lipid wrapper subtool, which allows the user to embed their channel in a membrane; and the boundary force potential calculator, which determines the potential energy barrier presented by the channel. The user can also download the acc and charge files produced by the map generator and lipid wrapper. Finally, the suite contains the biology Monte Carlo simulator, which simulates ion channel flow through the user provided channel. The user has the ability to change a number of parameters, including the transmembrane voltage, intra- and extra-cellular concentrations of Na+, Cl-, K+, Ca2+, and Mg2+, and the run time. A sample PQR file (of the gramicidin channel) can be downloaded to the right in the supporting documents section. Additionally, in the related resources secion below you can find a presentation on how the BioMOCA code works, as well as a practical guide explaining how to use the BioMOCA Suite. |
| Credits | Computational Electronics Group, University of Illinois at Urbanca-Champign. This work is funded by the NSF. |
| Cite this work | If you reference this work in a publication, please cite as follows:
In addition, we would appreciate it if you would add the following acknowledgment to your publication:
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| Version released | 01 May, 2008 |
| Type | Tools |
| Tags |
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1.6 Ranking Publications
Pratical Introduction to the BioMOCA Suite
Pratical Introduction to the BioMOCA Suite
Type Publications Contributor(s) David Papke Date 23 Apr, 2008 Avg. Rating (0) Rate this In this presentation, I describe how to use the online BioMOCA Suite. I explain how to prepare the .pqr input protein structure from a .pdb structure. I then explain in detail how to use each of the four subtools in the BioMOCA Suite. I do not cover in detail how the BioMOCA code works. If you are …
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