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Software
The Knime analytics platform (https://www.knime.org/knime) has been installed with all the free extensions.
It can be launch using desktop icon or from the terminal with knime command.
The following Knime extensions are available:
Fetch data from http://gpcrdb.org
See https://github.com/3D-e-Chem/knime-gpcrdb for more information.
Calculating distance of bitvector using Modifed Tanimoto similarity index.
See https://github.com/3D-e-Chem/knime-modified-tanimoto for more information.
Calculates subfamily specific two entropy analysis (ss-TEA) score. The ss-TEA can identify specific ligand binding residue positions for any receptor, predicated on high quality sequence information.
See https://github.com/3D-e-Chem/knime-sstea for more information.
Knime plugin for retrieving data from KLIFS (http://klifs.vu-compmedchem.nl). KLIFS is a structural kinase-ligand interaction database. For more information regarding KLIFS see the website.
KripoDB KNIME nodes for retrieving fragment information and similar fragments based on Kripo protein-ligand interaction pharmacophore fingerprints. Make use of KripoDB Python library.
The SyGMa KNIME nodes for the Systematic Generation of potential Metabolites. See https://github.com/ridderl/sygma for more information.
RDkit (http://rdkit.org) has been installed with Python bindings and PostgreSQL cartridge. It can be used in Python scripts, Knime workflows or Postgresql tables.
Python package called kripodb to use Kripo fragments, fingerprints and distance matrices is installed.
See https://github.com/3D-e-Chem/kripodb for more information.
The VM can be upgraded in 2 ways.
By running following command in a terminal inside the VM:
sudo vagrant_upgrade
This will run the latest provisioning scripts.
Make sure there are no applications open, as the application or machine might need to be restarted.
Destroying the current one and downloading a new one. The VM can be replaced by running the following commands in a vagrant prompt:
# In a terminal go to the directory in which you ran `vagrant up` previously, the directory should contain a file called `Vagrantfile`.
vagrant destroy
vagrant box update --box nlesc/3d-e-chem
vagrant up
Note! The vagrant destroy command will remove the Virtual Machine, including any changes that where made inside of it, but will keep the contents of the directory with the file called Vagrantfile.