This forum uses MediaWiki syntax, so I just thought to go through the very basic ones:
=== Small heading ===
* '''Bold''' list item, with a [http://www.bioclipse.net link].
* ''Italic'' list item, with some <code>preformatted text
will look like so:
=== Small heading ===
* '''Bold''' list item, with a [http://www.bioclipse.net link].
* ''Italic'' list item, with some preformatted text.
Hi,
When I use Balloon to generate 3D coordinates from an SDF table I end up with a file called 'xyz_3d.mdl'. This file contains 3 conformers for each entry in my original table (model 0, 1, 2 & model 3, 4, 5 & model 6, 7, 8 etc. in the 'outline' tab) .
In that way I loose all the info, e.g. molecule IDs, I have in my original table.
How can I keep this info or copy the 3D model back into the original table ?
Also, how can I generate just one 3D model ? ('Generate Conformers' and specifying 1 conformer does not help, but it generates 5 conformers)
Many thanks
Andreas
Upong generating 3D coordinates from an sdf-table I received the following error:
Balloon failed: Balloon timed out. Reason: null
I would be grateful for any help.
Many thanks
Andreas
Update:
After exiting Bioclipse and restarting the 3D coordinates suddenly appear.
1) Is there any way to import molecules from ChEMBL ?
2) Or a related question is: ChEMBL results can be downloaded as a table containing many columns including molecule ID and SMILES. Is there any way to import such a table into Bioclipse and generate the 2D molecular structures from the SMILES codes ?
Many thanks
Andreas
Hi,
I found you project while searching the internet for a free OS alternative to Vector NTI (VNTI)
http://www.invitrogen.com/site/us/en/home/LINNEA-Online-Guides/LINNEA-Co....
As you are probably aware of Invitrogen (owner of VNTI) has recently discontinued its free-license program for academic usage of VNTI after more than 3 years. You now need to pay more than 1000 GBP if you want to continue using that program.
Hi again,
I need a clue, how to import my own results of independently calculated values into bioclipse QSAR analysis.
greetings,
Filip
Hi,
first of all I would like to thanks for the great software!
Here I have a question regarding QSAR analysis. I managed to create columns with calculated descriptors and to create graphs biological_response vs. descriptor value. This way I can "optically" assess if the descriptor value has influence on biological response. But is there way to eg:
1) create plots for all calculated descriptors vs biological response
2) get some kind of relationship of ALL calculated descriptors vs biological response (eg IC50 = f(cLogP, M, molecular_volume, ...) ?
greetings,
Filip
How can I uninstall Bioclipse from my desktop computer running Windows XP.
Many many thank for the video It's very useful but (Yes there is a but).
It desn't works on my computer. I tried a several times with differents molecule format, ...
I delete all Bioclipse on my computer (Win XP) and re-dowloaded it.
The .csv and desciptorValues.xml never has been created.
I attach you an example: Warfarin .
Cheers,
Bertrand
We realized today that the frontpage, and some other pages, on www.bioclipse.net were broken.
Lucklily we had started work on setting up a new website, (based on Drupal) already, so because of the problems with the old site, we decided to quickly get a barebones Drupal website up running.
We're currently awaiting the implementation of a new design, done by Per Andersen (designer of e.g. pharmbio.org), which we look much forward to, so stay tuned!
