Miscellaneous Web Services enabling Open Notebook Science projects

ONS Projects

  1. Conversion from common name to CSID, density, MW, SMILES (sheet, description)
  2. CSID to Experimental Melting Point MP (°C) via url (example,all onsc compounds)
  3. Linear regression service - data passed via url (example)
  4. SMILES to length. Calculates the length of a molecule by first approximating the 3D atom coordinates via smi23d and then returns the maximum distance between all pairs of atoms plus their respective van der Waals radii from (http://periodictable.com/Properties/A/VanDerWaalsRadius.an.html). (example)

External Services
  1. Cactus NCI chemical name resolver (link)
  2. SMARTS viewer (link, discussion)
  3. SMILES viewer for multiple molecules - DEPICT (link)
  4. SMILES viewer - ambit (link, description )
  5. Molar volume - ChemAxon - must generate conformer first (link, discussion)
  6. CDK.web services (link)
  7. FROG 3D conformer generation from 2D input such as SMILES (link)
  8. Molar Volume with 3D coordinates returned as sdf - ChemAxon (example)
  9. Lilly Medchem Rules for identifying Potentially Reactive or Promiscuous Compounds (webservice, description, paper)
  10. OPSIN. Name to Structure Convertor (link)

Software

  1. SDF viewer - ChemFileBrowser from Hyleos (download)
  2. ChemCell - addon to Excel for converting common names to SMILES (description)

Partial Code

  1. Using Perl to query ChemSpider (link)
  2. Reordering SMILES atom order (link)