Q&A about 3DMET


General questions

1. What was changed from release 2.0 to release 2.1?

The data of release 2.1 are principally same to the release 2.0. The following point is different.
  • Manual curation was introduced to confirm 3D structures
    Automatical conversion often makes error about chiral atoms and/or bonds. Thus, we introduced manual curation step to develop 3D structures. After confirmation by using InChI and canonical SMILES, the structures not-chekable automatically were corrected and confirmed by manual. This information is also shown in the column of "Three-dimensionalizing operation" of each data page.

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

The data of release 1 and release 2.0 are largely different. The most important points are as follows.
  • Better 2D-3D converter
    The second change is the 2D-3D converters. The programs of CONCORD standalone was used in the release 2.0 (The programs of CONCORD sketch and MOE were used in the release1). The two programs were the best performance to convert structures among all methods we tested.

  • Confirmed 3D structures about chirality
    During 2D-3D conversion, many structures developed by several programs were changed about chirality. Thus, we have determined how to confirm conservation of chiralities. In the release 2.0, we use InChI and canonical SMILES to determination. These two programs were the best choice to be identified canonicalized compound structure among all methods we tested. This check had been performed by strings of unique SMILES by SYBYLTM and aRSChirality by MOETM in the release 1.

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

  • Visible 3D-structures from also Macintosh computer
    In the previous version, MDL Chime was used to visualize 3D structures. In this version, we adopt Jmol to be able to see the structures from any kinds of computers.

  • Probably different 3D-structures
    Because of change of the conversion methods, resulted 3D-structures may be different even if the same 3DMET ID. In the release 2.0, 3DMET recorded only the structures newly confirmed.

3. How to contact to 3DMET developers?

If you have any comments and questions, please freely ask us via "contact us" page. The answers to the general questions will be up to 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 in this server. Because of the licences for them, free bulk download is not permitted. However, it is not applied to the co-working. If you wish to use under this condition, please contact us from the contact page.