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MDB Improvement and Update History

• November 20, 2003 - Macintosh OS X users: please use Netscape rather than Safari or Internet Explorer for our "Search the MDB" viewer. The current Internet Explorer and Safari browers are not working correctly with our 3-D viewer. You can, however, perform queries with any browser using the Advanced search form and do statistical analyses using the statistical analysis tools, but the 3-D viewing is not available right now. (The problem appears to be recent changes in the implementation of JavaScript to Java communications and we are working on a solution. A similar problem has appeared on some [not all] Sun Solaris Netscape browsers - M Pique).
• August 2003 - Because of the constant spamming and flooding attacks to our server, we have reset the usage history for the MDB and are now actively filtering off these attacks from the logs. We have started doing this with the August 2003 logs.
• May 26, 2003 - A paper describing the ClusterGeom tool is now in print. This is a tool to analyze iron-sulfur clusters, and the paper describes the module that processes [4Fe-4S] clusters. The reference is:

  Fee, J. A.; Castagnetto, J.M.; Case, David A.; Noodleman, L.; Stout, C.D.; Torres, R.A.; "The circumsphere as a tool to assess distortion in [4Fe-4S] atom clusters". J. Biol. Inorg. Chem. 2003, 8: 519-526.
  On-line at: http://dx.doi.org/10.1007/s00775-003-0445-8

  Supplementary information on the equations, etc. can be found at our ClusterGeom page.
• April 03, 2003 - The talk "Data Sharing in Bioinformatics: Using the MDB's Web Services" is now online. This talk was given at the 225th ACS National Meeting (March 23-27, 2003) New Orleans, LA. (original summary). You can also download a PDF file of the presentation. More talks about the MDB in our "Talks" page.
• January 24, 2003 - The talk "Creating and Using Multi-protocol Bioinformatic Web Services" is now online. This presentation will be given as part of the Bioinformatics Technology Conference (February 3-6, 2003) San Diego, CA. (original summary). You can also download a PDF file of the presentation. More talks about the MDB in our "Talks" page.
• August 02, 2002 - New talks about the MDB online, one showcasing the new APIs for non-interactive use/access/embedding of the MDB data. See them all in our "Talks" page.
• July 20, 2002 - A set of MDB web APIs is being deployed, so other web sites, applications and scripts can talk to the MDB directly using a HTTP-based system, a XML-RPC server or a SOAP server. Should be officially available in early August.
• May 10, 2002 - Check out a prototype of our future MSE tool (Metal-binding Site Evaluator), and some of the QM/DFT data integration, in our Beta-test page.
• April 04, 2002 - Courtesy of Google, you can now search the pages hosted at the MDB site for keywords (for example: anhydrase, schema or msit) just like you would do when using Google.
• March 04, 2002 - Added an option to specify the output format for the results from the SQL query form. The default is to generate an HTML table, but you also get the results as comma separated values (CSV), or tab separated values.
• February 22, 2002 - When performing queries using the SQL query form, if you use the fields source_id or site_id, a link will be automatically made to see the corresponding sites using the MDB interactive viewer. Also, if you use the field metal_lig_dist, a distribution plot will be generated and appended at the end of the results table.
• February 15, 2002 - The SQL query form supports also queries using "SHOW" and "DESCRIBE" (actually the support have been there since about 6 months ago, I forgot to announce that at the time). So you can see what tables we have in the MDB, you will use: SHOW TABLES as a query term (the whole MDB schema is also available as a link from the SQL query form page), and to see what fields are in a particular table you will use DESCRIBE, for example, for the table site the query will be: DESCRIBE site.
• January 03, 2002 - The paper describing the MDB on Nucleic Acids Research is available:
  
  Castagnetto, J.M.; Hennessy, S.W.; Roberts, V.A.; Getzoff, E.D.; Tainer, J.A.; Pique, M.E. "MDB: the Metalloprotein Database and Browser at The Scripps Research Institute". Nucleic Acids Res. 2002, 30(1): 379-382.
  
  
• December 05, 2001 - Added some more features to the Advanced search form. It can now crossrefence the results against a local copy of the PDBSELECT list (from their September 2001 release). Also, you can indicate whether you want the results sorted by PDB ID, TITLE, COMPND or resolution, in ascending or descending order. To facilitate the rapid screening of results, we are now including the resolution (where available) in the result output, as well as not limiting the protein description to the first 200 characters (as we did in the past).
• November 30, 2001 - New and improved Advanced search form, it now includes a simple way of specifying ligand type and number as constraints for the metal-binding site search. You can perform queries which will find all 4-coordinated copper (cu) sites, in which at least 2 of the ligands are Histidines and exactly one is Water, or any other combination that fits your research problem. This will allow you to make more precise searches without having to learn any SQL :-). Your feedback will be much appreciated.
• November 28, 2001 - Modified the Advanced search form to perform more complex and flexible searches. Give it a try and report problems, if you encounter one
• November 16, 2001 - A presentation on using the MDB API to embed data and analysis results, will be given at the O'Reilly Bioinformatics Technology Conference (January 28-31, 2002) Tucson, AZ. See the presentation summary at the conference site.
• November 15, 2001 - Talks about the MDB online at the Talks page. You can see the slideshows online or download the presentations (StarOffice format).
• November 06, 2001 - (Beta) Added a simple search interface showing the results of using the MSIT program to index metalloproteins. This program automatically recognizes first and second shell residues in a metal site, as well as being able to reliably index clusters and multinuclear sites. Test it with your favorite metalloprotein.
• September 23, 2001 - Updated the MDB content using all structures from the PDB released as of Friday, September 21, 2001. The database now contains 5473 metal-containing proteins and 19,333 sites.
  
• June 7, 2001 - MDB and Web server hardware upgraded to Sun Blade 100 CPU.
• January 19, 2001 - Added new tables to the MDB database. We have now collected data that will allow dehomologized searches (using PDBSELECT and WHATIF SELECT), as well as crossreferences of ligand names and their entries in the HET LIST (from PDB). Torsions for selected residues (His, Asp, etc.) have been collected, for all proteins in the latest PDB release, this will allow us to compare trends in metal-binding sites with the rest of the proteins. For a peek at the current schema, view the current schema
  
• December 11, 2000 - Updated the MDB content using all structures from the PDB released as of Wednesday, December 6, 2000.

About the MDB

TSRI's Metalloprotein site Database and Browser (MDB) contains quantitative information on all the metal-containing sites available from structures in the PDB distribution. This database contains geometrical and molecular information that allows the classification and search of particular combinations of site characteristics, and answer questions such as: "How many mononuclear zinc-containing sites are five coordinate with X-ray resolution better than 1.8 Angstroms?", and then be able to visualize and manipulate the matching sites. The database also includes enough information to answer questions involving type and number of ligands (e.g. "at least 2 His"), and include distance cutoff criteria (e.g. "a metal-ligand distance no more than 3.0 Angstroms and no less than 2.2 Angstroms").

This database is being developed as part of a project whose ultimate goal is metalloprotein design, allowing the interactive visualization of geometrical and functional information garnered from the MDB. The database is created by automatic recognition and extraction of metal-binding sites from metal-containing proteins. Quantitative information is extracted and organized into a searchable form, by iterating through all the entries in the latest PDB release (at the moment: September 2001). This is a comprehensive quantitative database, which exists in SQL format and contains information on about 5,500 proteins.

The MDB has 3 web-based interfaces:

1. The interactive interface:
   A frames based interface that allows interactive searching and display of the results, via the CCMS/TSRI java-based macromolecular viewer.
2. An HTML forms interface:
   Three forms that will allow you to perform complex searches of the MDB. The results are shown as a list, with appropriate links that allow downloading of the VRML 2.0 or PDB formatted structure files corresponding to the metal site, an option to see the site in the java viewer, and a link to the web page of the corresponding protein at the PDB site.
3. An SQL interface:
   Allows you to type straight SQL statements to perform sophisticated searches of the MDB.

Known limitations

• The site information contains only first shell ligands, and does not recognize multinuclear or cluster sites. Thus, for example, a 4-Fe, 4-S cluster with 4 Cys ligands appears as 4 Fe sites, each with 4 S ligands. The next major release solves this problem (see the beta page for a preview).
• Irons in heme groups usually are identified as having extra ligating atoms, because of the distance cutoff used.
• Structures derived from NMR spectroscopy are represented in the MDB only by the "MODEL/ENDMDL" coordinate set that appears first in the PDB file.

Miscellaneous

• A clarification. In the search forms in this site, "number of ligands" refers to the number of atoms ligated to a metal center. The number of residues ligating to a metal will then be equal or less than that number.
• Any hydrogen atoms in the PDB file (seen frequently in NMR structures) are eligible to be included as ligand atoms, but hydrogens do not appear in the 3-D viewer.

NOTES:

1. If you want to cite the MDB, use the following reference:
   
   Castagnetto, J.M.; Hennessy, S.W.; Roberts, V.A.; Getzoff, E.D.; Tainer, J.A.; Pique, M.E. "MDB: the Metalloprotein Database and Browser at The Scripps Research Institute". Nucleic Acids Res. 2002, 30(1): 379-382 [http://metallo.scripps.edu]
   
   If you are referencing this web site, see the corresponding answer in the FAQs page.
2. If you want to see the source for our PHP scripts, see the FAQ entry showing you how to do that.
3. You can download the source of CCMS/TSRI Macromolecular java viewer (used in the interactive search interface) in tar.gz format, or in zip formats. The archives contain the java sources as well as the jar file with the compiled classes.
   If you cannot read these formats, e-mail us and we can send the source via plain text e-mail to you.
   This is stable beta code and Open Source (GPL).
4. We are also the US Mirror of the PROMISE site (from the University of Leeds).