Another great new feature to be introduced in ChemDoodle v1.4.0 is the new and improved MolGrabber widget. Notice that the “LITE” part of the widget’s name has been dropped. This is because the new widget is much more powerful than even the original MolGrabber web application. MolGrabber now has full access to all the data and powerful features that PubChem’s incredible database provides. When using ChemDoodle, you now have instant and convenient access to over 10 million chemical structures to include in your figures with amazing performance.

UPDATE: ChemDoodle v1.4.0 was released on 12/19/08.

First, let me discuss the new layout of this widget. It has been almost completely redone. Note that MolGrabber automatically formats structures to the current chemical document settings.

  1. There is now only 1 search field. This field can take any value, from an IUPAC name to a CAS number to an InChI string.
  2. You may choose to restrict your search to certain columns in PubChem’s database.
  3. A graphical spinner now keeps track of the busy status while contacting PubChem’s servers. The entire process is now multithreaded so that long queries no longer lock up ChemDoodle while they are running.
  4. Results now display more common names, molecular formulas are now formatted, and molecular weights are added to the description.
  5. MolGrabber now displays the total amount of results that match your query, as well as the current range.
  6. You can now page through the results until you find the one you were looking for, although it will most likely appear in the top 5 results, if not the first.
  7. MolGrabber will compile all the data from a single result and display it in a text area.
  8. All widgets, including MolGrabber, are now completely resizable.
  9. The maximize button will now enlarge widgets, as well as shrink and reposition them if they are already enlarged.

These improvements allow you to easily search for structures and quickly drag them right onto the Doodle Sheet. The improved search algorithm allows you to find almost any structure imaginable. And the new multithreaded functionality allows you to continue to work on your figures while MolGrabber is working on your query. In our testing, we noted that the average search lasted about 3 seconds, taking about 1 second to retrieve a result. This greatly improved widget beautifully unites a chemical structure database with a chemical drawing tool in an ingenious way that has never been done before. Sure, you could just search a database online to download a .mol file and then load it into your drawing tool, but now imagine the convenience ChemDoodle provides by eliminating the most tedious steps.

These capabilities are generously provided by the National Center for Biotechnology Information’s (NCBI) Entrez and Power User Gateway (PUG) systems. Through these services, MolGrabber can conduct a number of functions, from simple name searches to very complex substructure searches and mass calculations. So what is in store for MolGrabber in the future? Firstly, we now have very robust access to all of NCBI’s databases. At the moment, MolGrabber can perform simple searches and data retrievals. We will be adding more functions for advanced searches, complex substructure queries, and more intuitive ways to compile and analyze mass amounts of data. MolGrabber was also rebuilt in a way to provide convenient access to multiple databases. Communication with the Protein Data Bank is one of the next features on our list. Lastly, we are continuing to develop a tool that seamlessly merges all of the informatics tasks a chemist must perform with a drawing tool that is easy to use. We will continue to improve ChemDoodle in this aspect, and we know this improved database connectivity is a step in the right direction. Expect ChemDoodle v1.4.0 to be released in late November.

I should note, NCBI does have a few user requests; the relevant items are listed here:

User Requirements

Do not overload NCBI’s systems. Users intending to send numerous queries and/or retrieve large numbers of records from Entrez should comply with the following:

  • Run retrieval scripts on weekends or between 9 pm and 5 am Eastern Time weekdays for any series of more than 100 requests.
  • Make no more than one request every 3 seconds.
  • NCBI’s Disclaimer and Copyright notice must be evident to users of your service.  NLM does not claim the copyright on the abstracts in PubMed; however, journal publishers or authors may. NLM provides no legal advice concerning distribution of copyrighted materials, consult your legal counsel.