Q&A about 3DMET


General questions

1. What is new about Release 3?

The newly added entries (L-series) of Release 3 are collection from literature.
  • Fully manual curation was performed to develop 3D structures.
    L-series of entries were generated and checked by chemical curators. In Release 3.0, they were collected from several classical books describing natural products. We have a plan to add the further entries generated from newer information of academic papers.

2. What was changed from Release 1 to Release 2?

The data of Release 1 and Release 2.0 are very different. The most important points are as follows.
  • Better 2D-3D converter
    The 2D-3D converters were changed. The program of CONCORD standalone was used in Release 2.0 (The programs of CONCORD sketch and MOE were used in Release1). Among all methods that we tested, CONCORD standalone gave the best performance in converting structures.

  • Confirmed 3D structures with respect to chirality
    During 2D-3D conversion, many structures were changed with respect to chirality. We have determined how to confirm conservation of chiralities. In Release 2.0, we used InChI and canonical SMILES for these determinations. These two programs were the best choice for the identification of canonicalized compound structures among all methods we tested. In Release 1, this check was performed by strings of unique SMILES by SYBYLTM and aRSChirality by MOETM .

  • Increased descriptor numbers
    In Release 2.0, the descriptors were calculated by MOETM. The package can calculate many descriptors. Some descriptors in the previous version were substituted, such as CLogP (to logP(o/w) and SlogP) and CMR (to SMR).

  • 3D-Structures are visible from Macintosh computers
    In the previous version, MDL Chime was used to visualize 3D structures. In Release 2.0, we adopted Jmol which allows the structures to be viewed from all types of computers.

  • Possible differences in 3D-structures
    Because of changes of the conversion methods, the resulting 3D-structures may differ, even if the same 3DMET ID is used. In Release 2.0, 3DMET recorded only the structures that were newly confirmed.

3. How to contact the developers of 3DMET?

If you have any comments and questions, please ask us via the "Contact us" page. The answers to general questions appear on this page.

Frequently asked questions

1. Is it possible to download all 3D-structures of 3DMET?

Some commercial programs are used to convert 2D- to 3D-structures on this server. Because of the licenses for these programs, free bulk download is not permitted. If you wish to know the further information, please contact us via the contact page.