LC Collaboration Zone (LC CZ) Resources

Access to CPB resources

please apply for membership in the 'ncpbr' group here (lc-idm.llnl.gov).

Access to the AHA Protein Binding Atlas

The Protein Binding Atlas can be accessed through this link. Currently the site is open to all AHA Professional Members.

Access to GOSTAR Database and Focused Extraction Services 

Contact Marisa Torres(49) for GOSTAR searching

Contact Brian Bennion(1) for excelra data extraction

Access to the LLNL Small Molecule Datastore

TBD

 


Center Software Licenses and Downloads

Resource How to Access/Download POC

MOE-Molecular Operating Environment (Chemical Computing Group)

Site wide license accessible from LC CZ

/usr/workspace/ncpbr/software/moe2023/

Mac, Linux, Windows downloads for LLNL workstations/Laptops only 

bennion1@llnl.gov

Allchemy-Small molecule forward and retro synthetic Prediction

Cloud WebApp user licenses available upon request (<=20 in 2024)

bennion1@llnl.gov

Modeler-Protein homology modeling (Discovery Studio)

Access from LC CZ:

/usr/workspace/software/DiscoveryStudio/

Mac, Linux, Windows downloads for LLNL workstations/Laptops only 

One user license for use on LC CZ or LLNL workstations/Laptops (need license server info)

bennion1@llnl.gov

percepta-Small molecule physical property predictor (ACDLabs)

Access from LC CZ:

/usr/workspace/software/ACDLabs/

Mac, Linux, Windows downloads for LLNL workstations/Laptops only

One user license for use on LC CZ or LLNL workstations/Laptops (need license server info)

bennion1@llnl.gov

CGenff-Small molecule parameterization tool (Biosilcs)

Access from LC CZ:

/usr/workspace/software/BioSilcs/

Mac, Linux, Windows downloads for LLNL workstations/Laptops only

One user license for use on LC CZ or LLNL workstations/Laptops (need license server info)

bennion1@llnl.gov

Gaussian16,Gausview, Linda, GMMX -Small molecule ab initio calculator toolkits (Guassian.com)

Site wide license

/usr/workspace/ncpbr/software/gau16/

Mac, Linux, Windows downloads for LLNL workstations/Laptops only 

bennion1@llnl.gov

Haddock-CNS

Non commercial site wide license

Access from LC CZ:

/usr/workspace/ncpbr/software/Haddock

(spack packages available soon)

Mac and Linux downloads for LLNL workstations/Laptops only

bennion1@llnl.gov

AlphaFold

/p/vast1/alphafol

There's a README file in the above directory and a sample run file at

/p/vast1/alphafol/alphafold-2.3.1/run_script 

for batch jobs. This version of AlphaFold2 will only run on x86_64 machines and can use GPUs (Pascal).   

lau12@llnl.gov

Rosetta

/usr/workspace/ncpbr/software/rosetta

bennion1@llnl.gov

PyRosetta

/usr/workspace/ncpbr/software/pyrosetta

bennion1@llnl.gov

biorender

Limited seats for LLNL users

whalen3@llnl.gov

graphpad

Limited seats for LLNL users

whalen3@llnl.gov

 

 

Classified Resources

TBD

LC ISRD Resources

TBD

Additional Classified Computing Resources

TBD

 

For more information about the Center for Predictive Bioresilience software resources, please contact: Brian Bennion