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How to Use BindingDB


  1. How do I search BindingDB for small molecules that bind to my target protein of interest?
  2. How do I search for targets by the sequence of the protein or nucleic acid?
  3. How do I search by binding characteristics, such as Ki, KD, EC50, ΔG, and pH?
  4. How do I search BindingDB for proteins that bind my small molecule of interest?
  5. Can I search for a small molecule by its structure?
  6. How do I search for compounds based on their SMILES string?
  7. Can I download the full BindingDB dataset for a given protein Target? 
  8. How do I upload a list of compounds I’m interested in and find out what targets they might hit?
  9. Can I find FDA-approved drugs in BindingDB?
  10. How do I search by data source, such as author name, Institution, PubMed ID number, or PubChem BioAssay id?
  11. I found an interesting measurement. How can I download all other data from the same publication?
  12. How do I search BindingDB based on IDs from other sources, such as PDB, UniProt, Swiss-Prot, or PubMed?
  13. Can I download the entire BindingDB database?
  14. Can I enter my own compounds and binding data into BindingDB?
  15. Can I order compounds through your site?
  16. I am a developer.  Can I make links into BindingDB?
  17. How do I find data from a particular company?
  18. Are there any compounds in BindingDB for which there are data against multiple Targets?
  19. Are there links between BindingDB and 3D structures in PDB?
  20. Can I navigate from an article in PubMed to the data in BindingDB?
  21. Is there an on-line site to discuss BindingDB?
  22. What should I do if I think I've found an error in the data?

 

  1. How do I search BindingDB for small molecules that bind to my target protein of interest?

    Along the left-hand panel under Search and Browse, there are sub-categories for which the user can search by various items. Under the Target heading, the user is able to select the name of the protein by scrolling through the list, by choosing the first letter of the name, or by typing to search by the entire name http://www.bindingdb.org/bind/ByTargetNames.jsp.   A number of binding statistics are given for each target name, along with links to articles and other databases.  The user also has the option of downloading 2D or 3D SD Files of the molecules.

  2. How do I search for targets by the sequence of the protein or nucleic acid?

    BindingDB offers the users a BLAST search page that accepts input for an amino acid or nucleic acid sequence: http://www.bindingdb.org/bind/BySequence.jsp

  3. How do I search by binding characteristics, such as Ki, KD, EC50, ΔG, and pH?

    The user can further refine their search for a target by giving ranges for experimental data collected for inhibitors.  Choosing any of these items under the Target Name in the vertical menu links to a separate page for each characteristic.  The user can also search by molecular weight in addition to these binding data: http://www.bindingdb.org/bind/ByMolWeight.jsp

  4. How do I search BindingDB for proteins that bind my small molecule of interest?

    BindingDB allows users to filter targets based on the name of small molecules known to bind them. http://www.bindingdb.org/bind/ByLigandName.jsp.  This search also gives the user an option to add known binding characteristics, such as those described above.

  5. Can I search for a small molecule by its structure?

    Yes. The second item under the Compound heading of the vertical menu is Chemical Structure.  Here, the user can manually draw a compound or fragment and perform a 2D search from this.  The drawing is done using an embedded ChemAxon Marvin Sketch plugin: http://www.bindingdb.org/bind/chemsearch/marvin/index.jsp.    This page also gives the option of further customizing based on particular activity data, molecular weight, and target.  As you may have a collection of molecules tested experimentally but not yet published, the BindingDB molecular drawing feature gives users the ability to search the database for structural features that may exist in similar compounds.  The inclusion of Substructure or Similarity type criteria gives the user a powerful tool to infer binding modes based on specific structural moieties.  In addition, a filter can be applied to return only those results within a certain activity criteria.  The results are given as protein targets, with a number to the right of them indicating the number small molecule hits.  As before, 2D and 3D SD files can be downloaded for these hits.

  6. How do I search for compounds based on their SMILES string?

    An entry box allows users to input a SMILES (simplified molecular input line entry specification) string; http://www.bindingdb.org/bind/BySmiles.jsp.  The results have the number of small molecule hits listed next to the associated target name.   The output shows a Marvin 2D structure, along with a hit list of ligands and their targets.

  7. Can I download the full BindingDB dataset for a given protein Target? 

    Yes.  After going to the protein target search page and doing a search, http://www.bindingdb.org/bind/ByTargetNames.jsp, the user can then select a particular target name.  This brings up another page where a data set can be generated.

  8. How do I upload a list of compounds I’m interested in and find out what targets they might hit?

    The ‘Batch Structures’ link provides a search for multiple molecules in a user prepared file.  http://www.bindingdb.org/bind/BatchStructures.jsp.  This search can be set to substructure, similarity, or exact.

  9. Can I find FDA-approved drugs in BindingDB?

    Yes.  A list showing 2744 names of FDA approved drugs can be found here: http://www.bindingdb.org/bind/ByFDAdrugs.jsp.  The output is organized by name of drug, its active ingredient, links to public databases with drug information, and several properties of the drugs, which contain links to specific experiments and their respective data.   In the last column, links to 2D and 3D SD files is also available. 

  10. How do I search by data source, such as author name, Institution, PubMed ID number, or PubChem BioAssay id?

    A list of links under the ‘Data Source’ heading of the vertical menu reveals several ways of searching publication data including author name, Institution, PubMed ID, or PubChem BioAssay aid.

  11. I found an interesting measurement. How can I download all other data from the same publication?

    Once a search has been performed by PubMed Identification Number, http://www.bindingdb.org/bind/ByPubMed.jsp, the user can simply click on the number next to the article of interest listed in the Data column.  This number is a link to all of the data corresponding to that article in BindingDB, and selecting the ‘Make Data Set’ button at the top of the page generates a downloadable file.  

  12. How do I search BindingDB based on IDs from other sources, such as PDB, UniProt, Swiss-Prot, or PubMed?

    BindingDB provides links to other databases by simply clicking on the respective links under the ‘Other Databases’ heading of the vertical menu for PDB (http://www.bindingdb.org/bind/ByPDBids_100.jsp), UniProt (http://www.bindingdb.org/bind/ByUniProtids.jsp), and Pubmed (http://www.bindingdb.org/bind/ByPubMed.jsp) for cross-referencing data. 

  13. Can I download the entire BindingDB database?

    Yes. Selecting the Monomer List in CSV, http://www.bindingdb.org/bind/ByTargetMonomers.jsp shows all the protein targets, which can then be downloaded locally in a csv file.  As another option, HET list in SDF http://www.bindingdb.org/bind/ByTargetHets.jsp also allows the user to download all protein targets, this time as PDB coordinates.  In order to retrieve all the data in BindingDB, the link to ‘All Compounds and Data’ http://www.bindingdb.org/bind/chemsearch/marvin/PolicyNotice.jsp?all_download=yes  provides a downloadable data set of all compounds in BindingDB, with target and affinity data as 2D/3D SDF, FASTA, and other formats. 

  14. Can I enter my own compounds and binding data into BindingDB?

    BindingDB offers users an ability to enter their own data into our database.  This deposition can be accessed by links under the ‘Enter Data’ heading.  For example, entering new ITC data can be done here: http://www.bindingdb.org/jsp/forms/showLogin.jsp and a Form for new Ki data can be found here: http://www.bindingdb.org/jsp/forms_ki/showLogin.jsp.  The BindingDB team is actively working on a solution to allow experimental labs the ability to upload all their data to a customized user database.  This ‘MyBindingDB’ project will be available in the upcoming months.

  15. Can I order compounds through your site?

    No.  BindingDB is a digital resource of proteins and compounds made publicly available.  We do not house any experimental material locally.

  16. I am a developer.  Can I make links into BindingDB?

    Yes.  A description in our info page http://www.bindingdb.org/bind/SearchTemplates.jsp described the types of searches that can be done through BindingDB.  We welcome other suggestions that may assist your project.

  17. How do I find data from a particular company?

    BindingDB has a list of all universities, companies, and other intuitions that have binding data associated with them.  This link http://www.bindingdb.org/bind/ByInstitution.jsp provides a list of these entities, along with the number of enzyme inhibition, ITC data, and articles that originate from these sources.

  18. Are there any compounds in BindingDB for which there are data against multiple Targets?

    Yes.  As an interesting overview of the database, ‘Number of Data per Target’ shows how many targets are associated with each unique compound in the database: http://www.bindingdb.org/bind/ByTargetsLigand.jsp

  19. Are there links between BindingDB and 3D structures in PDB?

    Yes.  BindingDB collaborates with the RCSB PDB to provide access to proteins bi-directionally.  For instance, a search for the ABL protein, reveals 144 compound hits, and each entry has a target column with mulitple links to other databases (B.MOAD, Google Scholar, MMDB, PDB, UniProt) http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_ki.jsp?target=ABL&tag=tg&kiunit=nM&icunit=nM&column=ki&submit=Search&energyterm=kJ%2Fmole.  By clicking on the PDB link, the user is taken to the PDB website showing a list of all structure hits with ABL.  Clicking on one of these hits, like 2HYY http://www.rcsb.org/pdb/explore/explore.do?structureId=2HYY and then the ‘Links’ button at the top of this page http://www.rcsb.org/pdb/explore/externalReferences.do?structureId=2HYY reveals another page with external links.  Under the Ligand Features heading, there is a BindingDB link that brings you back to the familiar compound search by target using PDB ID http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pdbids.jsp?pdbids_submit=Search&pdbids=2HYY.

  20. Can I navigate from an article in PubMed to the data in BindingDB?

    Yes.  The BindingDB team also collaborate with PubMed.gov, to provide access for users wishing to seek binding data for compounds in a publication.  For example, after the abstract of a particular article, http://www.ncbi.nlm.nih.gov/pubmed/18342402, there is a ‘LinkOut’ heading that expands to show more links – one of which is ‘The Binding Database’.

  21. Is there an on-line site to discuss BindingDB?

    Yes.  Users can post comments, questions, and suggestions in the BindingDB Forum: http://www.bindingdb.org/forum/forum.jsp.  Feedback is greatly appreciated.

  22. What should I do if I think I've found an error in the data?

    Go to the "Reaction Details" or other page that contains the error, and use the error-report link at the bottom of the page to email us a report. The email you send will automatically include information identifying the problem data to us. Thanks in advance for your help with this.

 

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