CDD Vault Update: Add Prefixes, IUPAC Name Support, Neutralization and More

This is a minor release providing several useful new features and a few design and bug fixes.

Automatically add prefixes to molecule names, plate names, and batch external identifiers

In Data Import Step 2, you can now provide prefixes to prepend to, for example, every molecule name in the file. This is very helpful when the file contains a numerical vendor id, and you want to add a prefix that clarifies the source of that numerical id, thereby making it unique (e.g. 12345 to ASN-12345).

IUPAC name structure import

You can now manually register and batch import structures from files using IUPAC names. The support for IUPAC names even permits many common chemical names. Try typing in “isoniazid” as the molecule structure.

Explicit H removal now the default

When importing structures from vendor files, most explicit hydrogens are now removed by default (only bound, non-isotope, neutral, non-radical hydrogens that aren’t important for the display of stereochemistry are removed). We occasionally see structures in files with all hydrogens explicit, and we always get requests to remove the explicit hydrogens, so now that’s what will happen always.

Neutralize imported structure (Only for vaults NOT using CDD’s “registration system” module)

When mapping structures from a file, you can now specify that the structure be neutralized before import into your Vault. This is a useful standardization that will ensure that if you’ve already imported that structure as a neutral compound, you will not import a duplicate with a different charge.

Import salts from ASINEX library files (Only for vaults using CDD’s “registration system” module)

The chemical vendor ASINEX supplies SD files for their compound libraries in which the salt information is not present in the MOL file structure, but is instead noted in a separate text field. You can now map and import the salt information directly from this field. Hydrates are not currently supported, but will be supported in the next release, which we expect to deliver within a couple weeks.

Formula weight on Registered Compounds page (Only for vaults using CDD’s “registration system” module)

The batch formula weight is now provided in the list of registered compounds (both the web page and the downloadable version) accessible from Step 4 of a committed data import.

Manual registration of molecule structures using MOL files

You can now manually add structures using MOL files (in addition to SMILES or drawing the structure in the structure editor). You could always batch import structures as MOL files from SD files.

ChemAxon upgrade

We upgraded the ChemAxon toolkit and Marvin structure editor to their latest version (5.2.6).

Minor fixes and enhancements

On the Search page, we now display both the number of total matching search results (“matches”) and the total number of unique structures in the search results, if those two numbers are different. This should make it easier to compare the number of hits among various public or privately shared data sets. We plan to address this more thoroughly in a later release, grouping all results with the same structure into a single row.

The list of runs on the protocol page is now in reverse chronological order (rather than chronological order). You can now delete your own messages from the message board. More helpful back links have been provided for many pages throughout the site. Several cancel links that were not red now are. We now supply this page, a list of recent changes for each release.