Oak Storage Server instructions to get a copy of Aldrich Market Select database
Commercial compound databases tailored to use with Phase
Schrödinger has partnered with Enamine, MilliporeSigma, and MolPort to provide a Phase database of fragments, lead-like, near drug-like, and drug-like compounds available from Enamine's "Stock Screening Compounds Collection", MilliporeSigma's "Aldrich Market Select", and MolPort's "Screening Compound Database" respectively. The MolPort and Sigma DBs are about 800 GB and the Enamine one about 340 GB. The databases can be updated quarterly to ensure compound availability and enable out-of-the-box virtual screening. Top-ranked compounds from a virtual screen can be easily purchased by ID directly from the compound vendors. Learn more about Phase software.
The Stanford Libraries have purchased MilliporeSigma's "Aldrich Market Select" database which we are updating annually and storing on the Oak Storage Server. In order to use the Aldrich Market Select database with Schrödinger Phase software, you must copy the database into your Sherlock 32.0 space where Schrodinger is stored.
Instructions for copying Aldrich Market Select to Sherlock 3.0
Please note: Users need to be added to both the sw_schrodinger group on Sherlock and the Stanford workgroup oak:p-sul-schrodinger.
- Sherlock High Performance Computing Cluster access to Schrodinger software (only on Sherlock 2.0): Your PI must submit a request to Grace Baysinger. Requests should include SUNet IDs for everyone. Grace approves and forwards requests to the Stanford Research Computer Center to create a lab group account.
- Oak Storage Server access to Aldrich Market Select: If your lab group wants to access the Market Select database, please send a request to Grace Baysinger. She will add your SUNet ID so that you are able to access the directory where the Market Select database is stored (oak:p-sul-schrodinger) using Stanford's Workgroup Manager.
Access the CACDB (in read-only) anywhere on Sherlock at the following path:
It's just ready to go from there.
But if you want to copy the CACDB to your own storage space, you can use Globus in the following way:
1. Go to https://www.globus.org/app/transfer and select "Stanford University" then authenticate using your regular SUNet ID credentials using Duo.
2. A "Transfer Files" page will open, with two sides representing the transfer's source and destination.
2.a. On the left side, click on the Endpoint text field and select "SRCC Oak". As the Path, please use the full path to the SUL Schrodinger directory:
2.b. On the right side, click on the Endpoint text field and select "SRCC Sherlock". As the Path, a user can specify where he/she wants the CACDB directory to be copied on Sherlock. By default, the Sherlock Globus endpoint will show the $SCRATCH space (large temporary storage space on Sherlock that is purged after 6 months).
3. Please make sure that only the option "verify file integrity after transfer" is checked at the bottom. I don't recommend to select any other option.
4. When both left and right sides are configured, select the CACDB directory on the left side (Oak) and click on the right arrow to start the transfer of the full CACDB directory to Sherlock. A user can now close the window and an email will be sent when the transfer has completed (it might take a few hours).