Archive for the “feature plans” category
Update: Extending the datapage with QSPR / ADMET calculations
by Andras Stracz on December 8, 2011 • Tagged as: property calculation
Thanks for those who reacted to the earlier blog entry, your opinion is highly appreciated. However, it seems that there is not enough interest in QSPR / ADMET calculations, so we will not be working on it in the near future.
Leave your commentExtending the datapage with QSPR / ADMET calculations
by Andras Stracz on June 23, 2011 • Tagged as: property calculation
We are thinking about extending our property calculation datapage with Quantitative-Structure Activity Relationship (QSAR) and/or ADMET calculations.
We would like to collect the most popular and reliable state of the art approaches in the field providing an interface for the medicinal chemistry community where structural properties and their applications are available.
As an example, currently we are looking at the following equations from Current Medicinal Chemistry, 2006, 13, 2653-2667, Tingjun Hou et al:
- Blood-brain barrier penetration:
- Caco-2 apparent permeability coefficient:
Please help us with suggestions by filling the survey below or share your thoughts in the comments section!
3 commentsImplementing mobile interfaces
by Andras Stracz on May 30, 2011 • Tagged as: chemical search, document mining, property calculation
We are thinking about adding mobile interfaces to chemicalize.org so you can use chemicalize.org with your favorite smartphone or tablet.
Supported devices would include Android phones and tables, iPhones and iPads, Opera Mobile and Mini, Blackberry devices and many more.
Due to the limited screen size and different controls (i.e.: touch instead of mouse + keyboard) on these smartphones and tablets, we are planning a limited service – initially only chemicalizing webpages and calculating properties -, but we need your help to identify the important information on these pages.
Please help us finalize our plans with the survey below or share your thoughts in the comments section!
6 commentsExtending structure search with context
by Andras Stracz on May 30, 2011 • Tagged as: chemical search, text search
We are thinking about extending the chemical search service with this contextual search options. You could extend your structure search with other related structures (similar structures, substructures, superstructures, tautomers, etc…) and non-chemical text such as disease names or research areas.
Web search already provides a solution for this, but because it is powered by Google, searching with related structures is not possible. It can however search the entire internet, while our chemical search service is limited to our database.
To help with understanding how useful it would be, please help us with filling the survey below or share your thoughts in the comments!
6 commentschemicalize.org for MediaWiki
by Andras Stracz on May 30, 2011 • Tagged as: mediawiki, plugins
We are thinking about creating a plugin for Mediawiki (the content management system that powers wikipedia.org and most other wikis) that would allow chemicalizing wiki pages automatically. With this, selected pages of your wiki would get chemical structure recognition capabilities.
The features would very strongly follow the existing WordPress plugin: automatically process content when it’s being edited; displaying the processed version where recognized names are underlined and on mouseover displaying a tooltip with the 2D structure image of that structure.
Help us to find out how useful this is to you, please fill out the survey below or share your thoughts in the comments section!
3 commentsCustomizing calculation and search parameters
by Andras Stracz on May 30, 2011 • Tagged as: chemical search, property calculation
chemicalize.org currently provides only defaults or limited configuration for its services. We are planning to extend this with the ability to customize – and save to your profile – any calculation parameters and search options.
These customizations would expose a large number of settings provided by the underlying ChemAxon toolkits. We can use and combine these to create the customization options on chemicalize.org.
Regarding structure based calculations, this would mean that results on the datapage, e.g.: logD could let you define parameters such as: method, method weight, consider tautomers, precision of the results. (See wireframe example above). You can learn more about the available calculation parameters in the end user guide on chemaxon.com.
On the search pages, this means fine tuning search options, and filtering or sorting results by calculated properties (logP, pKa, etc…) of the hits. You can learn more about search options in the end user guide on chemaxon.com.
To help us finalize these plans, please fill out the short survey below or share your thoughts in the comments section!
2 commentsExtract molecules from PDF files
by Andras Stracz on May 26, 2011 • Tagged as: document mining, PDF
Update: Upcoming new feature – extract molecules from PDF files
To help understanding the chemistry in PDF files (research papers, white papers, patents, etc…), we are thinking about creating a new service for chemicalize.org that processes PDF files in the same manner as webpages. You could upload or link to a PDF file and get a modified version with the contained chemical structures highlighted and 2D structure image tooltips.
The technical challenge is threefold:
- displaying PDF files in a browser without requiring plugins
- modifying the PDF to deliver the same features as chemicalized webpages (i.e.: underline recognized names, add table of contents, etc…)
- in case of image based PDFs, perform OCR and accurately retrieve text for structure mining
For this reason, we ask for your feedback on how valuable this service would be to you. Please fill this short survey below or leave us a comment with your thoughts!
4 comments
