ZINC Database - emolecule repository
Why is it needed? Compounds that are available today can become unavailable in six months because of unavailability of the underlying reagents. For most vendors, the list of available compounds is significantly smaller than the list of compounds they have made in the past. If you are doing virtual HTS you are probably interested in a quick verification of predicted hits. So, it makes sense to know which compounds can be ordered quickly i.e turn-around time of 30 days or less.
Why is this a difficult task? Typically, this means maintaining databases of compounds and updating them on regular basis. In my experience, I have received updates from vendors as frequently as a dozen times an year to none at all. Staying up-to-date with chemical vendor catalogs can quickly become a daunting challenge for small labs and organizations who don’t have dedicated people for this purpose.
How does ZINC help? They stay up-to-date with vendors. At any time, you can download the original 2D vendor catalog from ZINC. They have grown significantly in size and use in the last 5 years. More consumers typically means lesser bugs and better updated catalogs.
Of course, ZINC allows you to download the 3D formats as well. I have not found any documentation on their 2D to 3D pipeline. It may be available upon request. Going from 2D to 3D is a whole bag of tricks. One could potentially glue together applications provided by software vendors such as Open Eye or Molecular Networks to create a 2D to 3D pipeline. While it is great to have your own pipeline as it enables greater control on bugs and issues, it is significant amount of algorithmic work. Therefore, for some organizations, having a ready to dock 3D format is a considerable time saving.
Any Gotchas? I have not found any useful information or discussion at the ZINC forums. Ideally, it would be good to know the quality of vendors. Are these vendor lists as up-to-date as they claim to be? What is the typical ordering time? Quality of drug like compounds is also an issue.
In ZINC’s 3D formatted database, the compounds are renamed using ZINC ID and any information about the original vendor catalog ID is lost. This can be tricky when ordering compounds from vendors. The vendor catalog ID can be retrieved by going to the original vendor catalog and matching the compound but this translates to extra algorithmic work.
Nutshell? Nevertheless this is the best free resource on the web that allows user to download latest vendor compounds for virtual screening. The closest competition, emolecules charges upwards of $20K for doing the same.
Source: biotechnorati.wordpress.com
Other online searchable by structure databases:
Compounds and Compound Libraries from TimTec
