Plans for the MDB

Short Term:

• Update the "packages" to reflect the new release [ IN PROGRESS ]
• Migrate the "edited" DB to the new query system [ SUPERSEDED ]
• Add some extra "filtering" options to the interface for the "raw" DB [ COMPLETED ]
• Add an "expert" interface, without the viewer, and with more options to search on (possibly implemented using only HTML). This will also allow the individual downloading of the query results [ COMPLETED ]
• Reorganization of the documents in this web site. [ IN PROGRESS ]

Long Term:

Viewer:

• Report atom/residue names
• Selectively display of atoms/residues
• Atom/residue labelling
• Model site superpositions with a quantitative measurement/threshold.
• Selective addition of bonds between atoms
• Selection of atoms/residues/models by geometrical/type criteria.
• User defined color schemes for selected parts of the model(s)

Query interface:

• Addition of a simpler HTML-only interface, which will allow the download of the results from the queries for off-line viewing using a PDB or a VRML viewer. [ COMPLETED ]
• Increase the number of options that can be used to query the database [ COMPLETED ]
• Eventually, change the main interface to allow set selections on-the-fly, via (for example) a tree representing different classification schemes or properties. In this way very interactive searches could be performed, with no separate query stages. The sites will appear to be always one click away, the interface acting as a window into TSRI's MDB.
• Use the AVS modules written by Tom Macke, for prototyping our SQL queries, and in particular the visual interface. In the end only a Java-aware browser will be needed to make use of this interface.

Database:

• Improving the metal site recognition algorithm to include the whole first, second and, eventually, third coordination shells. [ IN PROGRESS ]
• Adding geometrical information from the recognized metal site and environment. [ IN PROGRESS ]
• Extending the classsification and organization of both, the human-edited and the raw database.
• Generalizing our search algorithm
• Generating tools to aid the manual entering of database entries IN PROGRESS
• Creating tools and methods to validate and update the entries in the "raw" database [ IN PROGRESS ]
• Move, during the first year, to an SQL based database system, which will allow a more robust searh engine and a more flexible update and modification of the data. [ COMPLETED ]