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Chemoinformatics tools in the cloud?

Asked by , Edited by Egon Willighagen [ Admin ]

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?

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1 answer


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)
There are certainly other areas that I haven’t gone in to (de novo structure generation, reaction enumeration etc) which could be built from the above list, but more likely you’d want apps to be installed rather than (re)implementing them.

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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.

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