How To Use the Molecular Modeling Database (MMDB): find 3D protein structures bound to a specific chemical

  SEE ALL "HOW TO"  >>

 

  Retrieve protein structures that are bound to a specific compound (e.g., aspirin):

 

  Method 1:   Retrieve a chemical record of interest from the PubChem Compound database, then follow the Other Links:Protein Structures option to see 3D protein structures bound to the chemical of interest   example: start with the PubChem Compound record for aspirin (CID 2244)  

 

  Method 2:   Use the PubChem Structure Search tool to compare a query compound to the database and retrieve identical compounds, then open the PubChem record of interest and follow the Other Links:Protein Structures option   example: use PubChem Structure Search to retrieve aspirin and identical compounds  

 

  Retrieve protein structures bound to the query compound or to similar compounds (e.g., aspirin or chemicals like it):

 

  Method 3:   Retrieve a chemical record of interest from the PubChem Compound database, view its Related Structures/Similar Compounds, then follow the Other Links:Protein Structures option for the set of retrieved records (see note)   example: start with the PubChem Compound record for aspirin, then retrieve similar compounds  

 

  Method 4:   Use the PubChem Structure Search tool to compare a query compound to the database and retrieve similar compounds, then view the Other Links:Protein Structures option for the complete set of retrieved records   example: use PubChem Structure Search to retrieve aspirin and similar compounds