Brief Introduction

PADFrag (Pesticide&Drug Fragments) database is a special molecular database for biological-functional molecular fragments. It contains 1652 FDA approved drugs and 1259 approved agricultural chemicals and 5919 molecular fragments generated from them. A special link-point marked fragment database is created along with common database, which will be useful for fragment-linking project. The 3D structure, physicochemical properties, target information for these molecules are recorded in PADFrag. All fragments are mapped into pdbbind database based on molecular similarity and interaction energy with binding sites.

Browser Recommendation

We tested our database using different browsers on different systems (IE10 or later on Windows, Firefox on Windows, Mac OS and Linux, Google Chrome on Windows, Mac OS, and Linux, Apple Safari on Windows and Mac os) to assure the normal display. The testing results showed good compatibility.

Free Support

If you have any questions, bug reports, or suggestions on how we could make PADFrag more intuitive, powerful, or useful. please send us an email.

Index

• 1.Fragment Generation Protocol
• 2.Fragment Mapping Method
• 3.Browse PADFrag
• 4.Search PADFrag
• 5.Fragment Assembly Tool
• 6.FAQ

1.Fragment Generation Protocol

All Fragments in PADFrag are generated from FDA approved drugs and commercial pesticides, to improve the diversity of our fragment database, a cut and recombine protocol is used, All fragments are filtered by physicochemical rules and only fragments with proper physicochemical properties are retained, as link-points are always important for Fragment-linking, the original link-points for all these fragments are then marked.

2. Fragment Mapping method

Fragments in PADFrag are mapped with approved drugs and commercial pesticides, you can easily browse fragments contained in a specific drug or pesticide and drugs contain your interested fragment. Meanwhile, to shed lights to the biological function of a certain fragment, all fragments in PADFrag are mapped into 13283 protein-ligand complexes in pdbbind-cn database based on molecular similarity and interaction energy with protein, more than 100 pdb entries are recorded for each fragment.

Take benzene as an example, benzene is the most common fragments in drugs and pesticides with a frequency higher than 0.28, Benzene can be mapped to 511 drugs and 311 pesticides. Mapping of benzene to pdbbind result in 5256 entries in total. Lysozyme (4I7J) is detected as the most ideal binding target for benzene, for benzene is nearly full packaged by hydrophobic residues in the binding site. 5 residues, Ala99/Leu84/Leu118/Tyr88/Val87 are demonstrated as key residues for the binding of benzene. In fact, the bioactivity of benzene towards 4I7J are record in pdbbind as 480 uM.

3. Browse PADFrag

PADFrag can be displayed in two modes. In drug2fragment mode, information about the drugs or pesticides is displayed, together with all fragments contained in them. In fragment2drug mode, information about the fragment is displayed, together with a list for all drugs and pesticides containing this fragment, Each Fragments are mapped into pdb database based on similarity search and interaction energy between fragments and targets.

4. Search PADFrag

PADFrag can be retrieved though both a text-based keyword search and a structure-based similarity search. For text-based search, drugs and pesticides together with fragments match the keywords will be showed. For structure-based search, drugs and pesticide molecules with similar structure with your input structure as well as fragments contained in your input structure will be present. You can also refine your search by choosing some specific physicochemical characteristics for the compounds.

5. Fragment Assembly Tool

Fragment-linking method is one of the major strategies to assemble fragments into novel molecules. PADFrag can help you to build your own molecular library in web. The input is an user-defined core structure generated by JSME. Your selected fragments with proper Pysicochemical properties will be connected to the link point of your core fragment. Finally, molecular library will be generated and send to the user. These molecular library will be useful in drug design project like virtual screening.

6. FAQ