Tutorial for ChemDB

01. Text Search 02. 2D and 3D Structure Information 03. Result Download
04. Substructure Search and Filter 05. Similarity Search and Filter 06. Drug Classification Search
07. Transport a query to other DB 08. Building Blocks Functional Group Search
09. Pharmacophore Search
 
01. Text Search
1) Select "NCI" in main menu
2) Select "Text Search"
3) Select "CAS Registry Number"
4) Enter "5343-41-9"
5) Click "Search" button
 
TIP
1) Name/Synonyms
   - is: search exact name
   - begins: search names that start with a query
   - contains: search names that contain a query

2) CAS Registry Number
   - examples of incorrect query:
     005343-41-9, 5343419

3) Formula
   - search exact formula
 
02. 2D and 3D structure information

 

1) 2D and 3D structure information link
Result  Compound information  3D Conformers   3D Conformer information
  •  Basic Search Result is linked to  Compound information.
  •  Compound information is linked to  3D Conformers.
  •  3D Conformers is linked to  3D Conformer information and  Compound information.
  •  3D Conformer information is linked to  Compound information and  3D Conformers.
2) Compound Information in each database
   NCI database
1) Chemical information
2) ADME Properties (BBB & HIA)
3) Drug-likeness
4) 2D molecular descriptors
5) National Cancer institute Screen data
  • AIDS Antiviral screen - Conclusion
  • AIDS Antiviral screen - EC50 Results
  • AIDS Antiviral Screen - IC50 Results
  • Human Cancer Screen - logGI50
  • Human Cancer Screen - logTGI
  • Human Cancer Screen - logLC50
  • 6) Other DB links of this chemical
     
     
       Drug database
    1) Chemical information
    2) Experimental properties
    3) Drug Class
    4) ADME Properties (BBB & HIA)
    5) Drug-likeness
    6) 2D molecular descriptors
    7) Other DB links of this chemical
     
     
       PhysChem database
    1) Chemical information
    2) Experimental properties
    3) ADME Properties (BBB & HIA)
    4) Drug-likeness
    5) 2D molecular descriptors
    6) Other DB links of this chemical
     
     
       Available Chemicals and Building Blocks database
    1) Chemical information
    2) ADME Properties (BBB & HIA)
    3) Drug-likeness
    4) 2D molecular descriptors
    5) Suppliers
    6) Other DB links of this chemical
     
     
     
    03. Result Download
    Click "download(.sdf)" button in NCI Text Search Result  Select fields 
    Start download and confirm fields  Click "SDFILE DOWNLOAD" and Download
    04. Substructure Search and Filter
    In this lesson, you can learn how to extract drug-like library from substructure search result by using
    various filters such as drug-likeness filter, reactive functional group filter, and absorption filter.
    1) Select "NCI" in main menu.
    2) Click Open button , and
    then upload query structure file
    (*.mol).
    3) Select "Substructure".
    4) Select "Lipinski's rule" of Drug-
    likeness filter.
    5) Check "Reactive functional
    group filter
    ", and then select "Nitro
    group at least one
    " in Reactive
    functional group window.
    6) Select "Absorption filters".
  • Select "water solubility" and enter
    "10" in "from" box. ("from 10", >=10  is
    default.)
  • Select "HIA" and enter "from 70 to
    100".
  • Select "BBB" and enter "1" in "to"
    box. ("to 1",<=1 is default.)
  • 7) Click"Search" button.
    TIP
    1) Reactive functional groups filter
       - the meaning of "At least one" : Include only structures without the selected reactive functional
         group in search result
       - the meaning of "At least two" : Include structures without the selected reactive functional group or
         with the only one in search result
       - the meaning of "At least three" : Include structures without the selected reactive functional group
         or with one or two in search result
    05. Similarity Search and Filter
    In this lesson, you can learn how to search similar structures in the selected supplier database.
    Supplier information is provided in Available Chemicals database and Building Block database.
    1) Select "Available Chemicals" in main menu.
    2) Draw the example query structure on drawing area.
    3) Select "Similarity using chi1 & chi3".
    4) Select Asinex, interbioscreen, SPECS  of
    Suppliers.
    5) Click "Search" button.
     
    TIP
    1) Yon can multi-select suppliers.
    06. Drug Classification Search
    In this lesson, you can learn how to search using Drug Classification of Drug database.
    1) Select "Drug" in main menu.
    2) Select "Drug Classification Search"
    3) Click Anti-arthritic, and then Click
    Antibacterial
    with 'Ctrl' key.
    4) Click "Search" button.
     
    TIP
    1) Yon can multi-select to maximum five classes.
    07. Transport a query to other DB
    In this lesson, you can learn how to transport a query used in a database or chemical structure of
    search result into the query page of other databases.
    1) Click 1st compound of Drug Classification
    search result to open information page.
    2) Select "Available Chemicals" of "Transport structure to query page of"
    3) Transport one of Drug Classification Search
    Result to query page of Available Chemicals database.
    4) You can search similar structures to drug
    in Available Chemicals database.
    08. Building Blocks Functional Group Search
    In this lesson, you can learn how to search using Functional group of Building Blocks database.
    1) Select "Building Blocks" in main menu.
    2) Select "Functional Group Search"
    3) Click Benzimidazoles.
    4) Click "Search" button.
     
    TIP
    1) Yon can select only one of functional groups.
    09. Pharmacophore Search
    In this lesson, you can learn how to search using Pharmacophore query.
    1) Define Pharmacophore Query and start search
    1) Select "Drug" in main menu.
    2) Select "Pharmacophore Search" in left
    menu of Drug database.
    3) Click "Open" button and upload 3D mol
    file.
    4) Select atom, and then click Donor
    button.
    5) Select atom, and then click
    Acceptor
    button.
    6) Select atom, and then click Aromatic button.
    7) Click Search button.
     
    Aspirin Pharmacophore Query
     
    2) 3D Conformers of Pharmacophore Search Result