How to Build Chemical Substance Database?
By Tatsuya Nakano (nakano@nihs.go.jp) modified by Kaminuma
Lecture note used at The Fifth GINC (Global Information Network on Chemicals, Tokyo Meeting,
Regional Webmasters’ Workshop, 22-25 February 2000, National Institute of Health
Sciences(http://www.nihs.go.jp/), Tokyo, Japan, 23 February 15:30-17:00
Contents
1.
Web Browser …………………………………………………………… 2
Microsoft Internet Explorer 5.01
Asian Language Fonts for Microsoft Internet Explorer 5.01
2.
Adobe Portable Document Format (PDF)
…………………………
6
Adobe Acrobat Reader, (Adobe Acrobat)
3.
HTML (HyperText Markup Language) ……………………………..
4.
Drawing chemical structure, and convert it to picture image
7
and 3D structure ……………………………………………………….. 8
4.1. Drawing
10
chemical
structure
……………………………………...
ISIS/Draw, (ChemDraw)
4.2.
Convert 2D structure to picture image …………………………
11
WebLab ViewerLite, (ChemDraw, ChemWeb)
4.3.
Convert 2D structure to 3D structure …………………………..
15
WebLab ViewerLite, (Chem3D)
4.4.
Convert 3D structure to Virtual Reality Modeling Language
(VRML) ……………………………………………………………..
17
WebLab ViewerLite
5.
Display molecular 3D structure on Web…………………………….
19
Chem3D Net Plugin 4.0, (Chemscape Chime )
6.
Simple Standalone Chemical Substance Database ……………….
21
6.1. Chemical Abstracts Service (CAS) Registry Number ………... 24
6.2. Simple Chemical Substance Database with Access ………….. 25
7.
Chemical Substance Database on World Wide Web ………………
30
7.1. MIME (Multipurpose Internet Mail Extensions) Map ……….
30
7.2. Web Publish Folder ………………………………………………..
32
7.3. MS Access Workgroup Administrator …………………………..
33
7.4. Access User Account ………………………………………………. 33
7.5. ODBC Driver ……………………………………………………….. 33
7.6. Simple web database with Active Server Pages (ASP) ………. 35
7.7. ChemOffice WebServer Ultra 2000 ……………………………. 37
1. Web Browser
Microsoft Internet Explorer 5.01
http://www.microsoft.com/
Asian Language Fonts for Microsoft Internet Explorer 5.01
2. –3. deleted
4. Drawing chemical structure, and convert it to picture image and 3D structure
GIF Data
JPEG Data
PNG Data
Conversion
ChemDraw
WebLabViewer
Generation
ChemDraw
ISIS/Draw
Display
MDL Chemscape Chime
WebLab Viewer
2D Structure Data
MDL Mol Format (.mol)
ChemDraw Format (.chm)
DB Search
Conversion
ISIS/ACD-3D
ISIS/NCI-3D
ChemFinder
WebLabViewer
Chem3D
Generation
3D Structure Data
MDL MOL format (.mol)
PDB Format (.pdb)
Chem3D
WebLab Viewer
Insight II
Refinement
Molecular Computation
DB Search
Molecular Mechanics Method
Molecular Dynamics Method
Molecular Orbital Method
How to Generate Structure Data
There are many molecular structure file formats. For example,
Protein Data Bank (PDB) format
http://www.rcsb.org/pdb/index.html
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html
CSD
ISIS/ACD-3D
ISIS/NCI-3D
PDB
MDL MOL format
http://www.mdli.com/cgi/dynamic/welcome.html
http://www.mdli.com/downloads/literature/ctfile.pdf