Accelrys provides small molecule databases to be used with Catalyst. The ABCC has licenses for the following databases from Accelrys: Chemicals Available for Purchase (CAP) Screening 2006, CAP Reagents, NCI2000, Maybridge2004, Mini-Maybridge. For more details about these databases, see below. Currently, we have these databases installed on an SGI server (500 MHZ IP35 Processors CPU:MIPS R14000). Because of this old technology, database searching via Catalyst becomes very difficult and in some cases even impossible. Discovery Studio 2.1 (DS21, latest version of DS Modeling software) now has all of the Catalyst modules (called within DS21 as Catalyst Components Collection) 3D-database searching can now be carried out using DS21. We have recently installed these databases on a Linux server (xeabc000.ncifcrf.gov). ABCC users should start using Discovery Studio 2.1 for their Pharmacophore Modeling projects.

How to access these databases?

These databases are typically accessibile via Discovery Studio 2.1 client desktops (running Windows or Linux OS). If you do not have DS21, then visit, the ABCC Feed-back and Issues wepage,http://www.abcc.ncifcrf.gov/issues/issue_frm.php and let us know that you are interested in using DS21. Someone from the ABCC will send you the ABCC-PC-Software link (http://pcsoftware.abcc.ncifcrf.gov/ ) along with the required username/password for downloading the software. Installation instructions (for windows) are available from the ABCC PC Software link, and can also be downloaded from here. Installation instructions for installing DS21 under the Linux platform can be obtained from here. From the DS21 server/client (ie. a desktop running Windows XP OS) one could do the following to access ABCC databases:

• Start DS21
  • Note: Usually "local host" (see Fig1 (low right corner)) means the current machine in which DS21 background calculations will be executed.
• To see the databases installed on the linux box File -> Change Server -> xeabc000@ncifcrf.gov:9943 [See Fig3 (low right corner)]
  If there are no errors, then you should access databases and do search on the databases as if it is installed locally. If you have errors at this step, email me at sravi@ncifcrf.gov. If not, move to the next step.
• To carry out 3D Database search, go to Protocols explor, expand the Pharmacophore protocol, and double click on "Search by 3D Database"
  • If you dont see Protocols Explorer, then click on View -> Explorer -> Protocols
• In the newly opened parameter box, Click on the "Input Database" on the "Parameter Value" box to choose the database of your interest (You should see, NCI2000, minimaybridge, Maybridge2004, CAPS2006, CAPR2006, BioByteMasterfile2001, sample databases. If you dont see all these databases, then you are not connected to ABCC linux node xeabc000.ncifcrf.gov. )
• In the "Input Pharmacophore" box, click on ... to open "Specific Query" box and choose "Query from a file", browse and choose a pharmacophore file of your choice (if you dont have a pharmacophore, click here to download the sample pharmacophore (ang-IIHypo.chm file) to your Desktop, browse and read the pharmacophore in), and click OK to return back to "Search 3D Database" box. Keep the rest of the options default, and click run
• After the job is done, go to Jobs explorer and double-click on the finished job to open the job summary, and click on ViewResults.pl to view the result.
• For more information on the analysis, use help in DS21.

Chemicals Available for Purchase (CAP) Screening 2006

Number of compounds      =   2542203
Disk space required:              34 Gb 
 

Properties Registered

PRICES
PHYS_PROP
LOG_P
COMPANY_CODE
PURITY
PRODUCT_NAME

Chemicals Available for Purchase (CAP) Reagents 2004

Number of compounds      =   220,902 
Number of fragments      =   240,803 
Number of conformers     = 9,386,022 
Average molecular weight =       350.07 
Average number of conformer 
per fragment             =        38.97 

Click here for more detailed information on the contact information of companies which has Chemicals Available for Purchase (CAP) Reagents.

Properties Registered

CAP KEY 
Conventional names 
Physical properties 
Supplier catalog entries 
Prices 

NCI2000

No. of compounds:        238,819 
No. of fragments:        252,032 
No. of conformations:  8,996,912 
Average MW:                  310.560 
Average no. of conformation 
per fragment:                 35.690 
Disk space required:               2.5 Gb 

Properties Registered

Molecular Weight 
Molecular Formula 
Internal Compound Name 
NSC 
CAS_RN 
AVS_CONC 
AVX_IC50 
NLOGG150 
NLOGGLC50 
NLOGTGI

Maybridge 2004

No. of compounds:                       59,652 
No. of fragments:                       61,011 
No. of conformations:                1,925,068 
Average MW:                                332.224 
Average no. of conformation 
per fragment:                               31.5528 
Disk space required:                       556 MB 

Properties Registered

Molecular Weight 
Internal Compound Name

MiniMaybridge

Small subset of Maybridge. The database that comes
with Catalyst and DS2.0

Sample

Small database that is part of CATALYST tutorials

Acknowledgements

I would like to acknowledge Dennis Foley and Fred Connner for helping me with some system administrative tasks. I would also like to thank Alan Lopez; Luke Fisher from Accelrys Inc. for their continuous support during our Catalyst database migration to the Linux platform.

Contact Info

If you have any questions or suggestions about the Catalyst Database, feel free to contact S. Ravichandran or Bob Lebherz at sravi@ncifcrf.gov / lebherz@ncifcrf.gov

Discovery Studio 2.0 can be downloaded from the ABCC-PC-Software link:

http://pcsoftware.abcc.ncifcrf.gov/ 

Please note that the the ABCC-PC- software link is a password protected site, please contact the ABCC HelpDesk ((helpuser@ncifcrf.gov / 301-846-5555 ) if you have any questions about this link or need a username/password.