If you wanted to develop/provision a Chemoinformatics Virtual Laboratory in the cloud, which chemoinformatics tools/applications does the community feel ought to be minimally present in such a laboratory?
rajarshi guha
[ Editor ]
from North Bethesda, United States of America
It’s going to depend on what the virtual lab is going to be doing, but a few core components come to mind (just focusing on free/OSS though I include non-OSS items for depiction/vis)
- low level libraries (OpenBabel, CDK, RDKit, Indigo)
- RDBMS + chemistry cartridge
- math/stats ®
- Conformer generation (Balloon, OpenBabel)
- Filtering tools (Strip-it, Siphonify)
- Docking tool (Autodock+VINA)
- Depiction and vis (JMol, JChemPaint, Marvin, ChemWriter, Pymol)
- Descriptor calculator (CDKDescUI, PaDeL)
- Pharmacophore search (Pharmer, CDKPsearch, Spectrophore)
- 3D QSAR (Align-it, Open3DQSAR)
NN comments
Nico Adams
-
Thanks Rajarshi. I appreciate the question was very general – I wanted to see whether there was a consensus set of software/functionality that people felt absolutely needed to be in any VL.