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Showing posts with label BioFET-SIM. Show all posts
Showing posts with label BioFET-SIM. Show all posts
Thursday, October 11, 2012
Monday, August 20, 2012
PyMOL on the iPad
I just got an email (labeled as spam for who knows reason) from Schrödinger saying that they made PyMol available for the iPad, and most of all for free. Now, who am I to resist and not try it head on? In fact I downloaded it immediately.
First impression: very negative! It starts with a very condensed help panel, closing which one should see a demonstration molecule. The molecule did not show up because the app says that I have not enough free memory on my device! So, here we have me with big expectations staring at a black screen with just a couple of buttons on the top. So sad.
Never mind, I decided to try and load another protein structure from the pdb. Second impression: amazing! One can finally "touch" proteins, rotate and move and zoom them as one wishes. There are the familiar ways of displaying a structure (e.g. lines, cartoon etc., but not ball-and-sticks for non ligands) and many possibilities for performing a selection. It is only 10 minutes that I'm playing with it, so I haven't figured out all the available tools. One thing I tried is to ray trace (yes, ray tracing!) the actual scene I had. The app miserably crashed.
My guess is that the app could become a nice tools for both (self-)education and production of nice images.
Here is my good-bad list after 10 minutes of playing around:
good
- possibility to load structures from many different sources (pdb, dropbox and others)
- possibility for different rendering
- possibility to directly save screenshots
- multiple structures can be displayed
- but most of all you can rotate them with your finger tips!
bad
- it seems it requires a lot of memory
- no possibility (at least I haven't found out) to fade out parts of the structure other than that one is interested in
One more thing: it would be soooooo great if Schrödinger would distribute the code behind the structure visualizer. It would open up many possibilities for visualizing a structure inside another app. Think like BioFET-SIM 2.0 on the iPad...
First impression: very negative! It starts with a very condensed help panel, closing which one should see a demonstration molecule. The molecule did not show up because the app says that I have not enough free memory on my device! So, here we have me with big expectations staring at a black screen with just a couple of buttons on the top. So sad.
Never mind, I decided to try and load another protein structure from the pdb. Second impression: amazing! One can finally "touch" proteins, rotate and move and zoom them as one wishes. There are the familiar ways of displaying a structure (e.g. lines, cartoon etc., but not ball-and-sticks for non ligands) and many possibilities for performing a selection. It is only 10 minutes that I'm playing with it, so I haven't figured out all the available tools. One thing I tried is to ray trace (yes, ray tracing!) the actual scene I had. The app miserably crashed.
My guess is that the app could become a nice tools for both (self-)education and production of nice images.
Here is my good-bad list after 10 minutes of playing around:
good
- possibility to load structures from many different sources (pdb, dropbox and others)
- possibility for different rendering
- possibility to directly save screenshots
- multiple structures can be displayed
- but most of all you can rotate them with your finger tips!
bad
- it seems it requires a lot of memory
- no possibility (at least I haven't found out) to fade out parts of the structure other than that one is interested in
One more thing: it would be soooooo great if Schrödinger would distribute the code behind the structure visualizer. It would open up many possibilities for visualizing a structure inside another app. Think like BioFET-SIM 2.0 on the iPad...
Saturday, August 18, 2012
Accepted in PLoS ONE: BioFET-SIM Web Interface: Implementation and Two Applications
Our revised version of BioFET-SIM Web Interface: Implementation and Two Applications has been accepted in PLoS ONE
Monday, August 6, 2012
Revised version of BioFET-SIM Web Interface: Implementation and Two Applications
A revised version of "BioFET-SIM Web Interface: Implementation and Two Applications" (Martin's second PLoS ONE paper) has been re-submitted to PLoS ONE and deposited at arXiv.
Our comments to the reviewers are summarized here.
In the process the web interface was significantly improved and Martin's has made some new screencasts:
Our comments to the reviewers are summarized here.
In the process the web interface was significantly improved and Martin's has made some new screencasts:
Monday, July 23, 2012
BioFET-SIM Instruction Videos
The BioFET-SIM web interface operation is illustrated in 4 short instruction videos:
Basic interface operation
BioFET-SIM signal and pH response calculation
Custom structure upload
Restoring a previous session
Feel free to contact us in case of any questions under
biofetsim at gmail dot com
Basic interface operation
BioFET-SIM signal and pH response calculation
Custom structure upload
Restoring a previous session
Feel free to contact us in case of any questions under
biofetsim at gmail dot com
Friday, May 4, 2012
BioFET-SIM Web Interface: Implementation and Two Applications
Martin submitted a new paper to PLoS ONE:
BioFET-SIM Web Interface: Implementation and Two Applications Martin R. Hediger, Jan H. Jensen, Luca De Vico. arXiv biofetsim.org
The paper was submitted April 27 and deposited on arXiv the same day.
Abstract
We present a web interface for the BioFET-SIM program. The web interface allows to conveniently setup calculations based on the BioFET-SIM multiple charges model. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orien- tation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.
Martin made a really nice screencast of the interface.
BioFET-SIM Web Interface: Implementation and Two Applications Martin R. Hediger, Jan H. Jensen, Luca De Vico. arXiv biofetsim.org
The paper was submitted April 27 and deposited on arXiv the same day.
Abstract
We present a web interface for the BioFET-SIM program. The web interface allows to conveniently setup calculations based on the BioFET-SIM multiple charges model. As an illustration, two case studies are presented. In the first case, a generic peptide with opposite charges on both ends is inverted in orien- tation on a semiconducting nanowire surface leading to a corresponding change in sign of the computed sensitivity of the device. In the second case, the binding of an antibody/antigen complex on the nanowire surface is studied in terms of orientation and analyte/nanowire surface distance. We demonstrate how the BioFET-SIM web interface can aid in the understanding of experimental data and postulate alternative ways of antibody/antigen orientation on the nanowire surface.
Martin made a really nice screencast of the interface.
Wednesday, August 10, 2011
New Paper: BioFET simulation with a multiple charges model
Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensor
De Vico L., Iversen L., Sørensen M. H., Brandbyge M., Nygård J., Martinez K. L., Jensen J. H.
Nanoscale, DOI: 10.1039/C1NR10316D
Abstract: A single charge screening model of surface charge sensors in liquids (De Vico et al., Nanoscale, 2011, 3, 706-717) is extended to multiple charges to model the effect of the charge distributions of analyte proteins on FET sensor response. With this model we show that counter-intuitive signal changes (e.g. a positive signal change due to a net positive protein binding to a p-type conductor) can occur for certain combinations of charge distributions and Debye lengths. The new method is applied to interpret published experimental data on Streptavidin (Ishikawa et al. ACS Nano 2009, 3, 3969-3976) and Nucleocapsid protein (Ishikawa et al. ACS Nano 2009, 3, 1219-1224)
We analyze how appropriate combinations of buffer conditions and charge distributions and orientation may lead to a counter-intuitive signal in BioFETs.
De Vico L., Iversen L., Sørensen M. H., Brandbyge M., Nygård J., Martinez K. L., Jensen J. H.
Nanoscale, DOI: 10.1039/C1NR10316D
Abstract: A single charge screening model of surface charge sensors in liquids (De Vico et al., Nanoscale, 2011, 3, 706-717) is extended to multiple charges to model the effect of the charge distributions of analyte proteins on FET sensor response. With this model we show that counter-intuitive signal changes (e.g. a positive signal change due to a net positive protein binding to a p-type conductor) can occur for certain combinations of charge distributions and Debye lengths. The new method is applied to interpret published experimental data on Streptavidin (Ishikawa et al. ACS Nano 2009, 3, 3969-3976) and Nucleocapsid protein (Ishikawa et al. ACS Nano 2009, 3, 1219-1224)
We analyze how appropriate combinations of buffer conditions and charge distributions and orientation may lead to a counter-intuitive signal in BioFETs.
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