Technical Information

Manual curation

  1. All structures of the COMPOUND database could not be converted correctly. Thus, manual curation was introduced from release 2.1.
  2. The structures not convertable automatically were checked by curators who have educated in the chemical or pharmaceutical course.
  3. The information is described in the "Three-dimensionalizing operation" columns.

How to define natural metabolites

  1. All structures of this version of database (release 2.0) is based on the COMPOUND database, a part of the LIGAND databaseL1 in GenomeNet, including 2D structure files written by MDL mol (SD) formatL2 .
  2. From all of the 2D structures files of COMPOUND database, the entries with the description of "R", "n" and "X" in the formula column were removed because the structures are not able to be identified.
  3. The natural compounds were chosen if applied to one of the following conditions.
  4. The entries having some harogens (F, Cl, Br) were deleted from the chosen entry set.

How to convert from 2D mol files to 3D files in 3DMET

  1. Two dimensional mol files of the COMPOUND database were transformed to three- dimensional structures (SYBYL mol2 format) by CONCORD standalone P1.
  2. The 3D structures from CONCORD standalone were minimized by SYBYL P2 (version 7.2) minimizer.
  3. MOEP3 (version 2009.10) were used to three-dimensionalize and minimize the structures when manual developing.
  4. The 3D-structure files were converted to the PDB format by using Open Babel P4 and recorded to 3DMET.

How to evaluate conserved two structures

  1. Both of InChIP5 (version 1.00) and canonical SMILES P6 (Daylight Software Version 4.94) strings were calculated from two kinds of 3D structures.
  2. The InChI and canonical SMILES strings were compared between 2D-structures and 3D-structures. The chirality description about phosphate was ignored.
  3. Compounds with the conserved structures and chiralities between two structures before/after conversion were picked up for 3DMET.
  4. If the chirality tags exist in ony 3D-structures, the structures were judged as conserved structures.

How to calculate molecular descriptors

  1. The descriptors of the structures were calculated by MOEP3 (version 2009.10).

Literatures (L1-L2)

  1. COMPOUND: Goto, S., Nishioka, T., and Kanehisa, M., LIGAND: Chemical Database for Enzyme Reactions. Bioinformatics, 14, 591-599 (1998)
  2. MDL mol (SD) format:

Programs (P1-P5)

  1. CONCORDTM: Optive Research, Inc., Austin, TX, USA (Now, joined to Tripos L.P.).
  2. SYBYL: Tripos L.P. St. Louis, MO, USA.
  3. MOETM (Molecular Operating Environment): CCG (Chemical Computing Group) Montreal, Canada.
  4. Open BabelTM: Open Babel developing project.
  5. InChITM (The International Chemical Identifier): www.InChI.com (the Laboratory of Chemical Informatics of the Institute of Chemical Technology , Prague, Czech Republic.
  6. SMILESTM: Daylight Chemical Information Systems, Inc., Aliso Viejo, CA, USA.

Acknowledgement

  1. The 3D-structures of this database was made from the 2D-structure-files of the Ligand/Compound database in the GenomeNet server.
  2. Calculation by MOE is performed on the server in the Computer Center of the Ministry of Agriculture, Forestry, and Fisheries.
  3. JME editor, using to exchange from drawing picture to SMILES string in this page, was kindly provided by Peter Ertl, Novartis AG.
  4. This database is published via NIAS DNA BANK.