SCOP
From Informatics
- What labs or how many are using SCOP?
- Honig lab
- Who is the main “database authority” for SCOP?
- Kely Norel (rn98<at>columbia.edu)
- What kind of database is it? (flat-file, relational, XML, etc)
- flat-file
- Size of database?
- 16 G
- Anticipated yearly growth? (Megabytes/Gigabytes)
- Backup procedures? How often?
- Database backups (Hot, Cold, Both) [and/or]
- Operating system backup
- OS backup
- What servers/operating systems are hosting them (IP addresses)
can't predict
- IP = 156.145.30.88 > vesta
- Red Hat Enterprise Linux AS release 4 (Nahant Update 3)
- Approximately how many *active* users?
- How often is the database used? (Daily, Weekly, Monthly)
- number of users in the Honig lab ~ 15
- What platforms are being used? (Oracle, MySQL, PostgreSQL, etc)
- N/A
- What applications are using these databases?
- Web interface?
- Application (GUI)?
- Command line interface (CUI)?
- command line interface
- daily
- Is it accessible from outside the firewall to public users?
- no
- What is the primary purpose of the database & types of data stored?
- The SCOP database provides a detailed and comprehensive description of all known protein structures
- The classification is on hierarchical levels: the first two levels, family and superfamily, describe near and far evolutionary relationships; the third, fold, describes geometrical relationships.
- The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to the SCOP database.
- The database can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures.
- Are there any issues or problems with the database?
- Specific error messages popping up?
- Problems connecting from the application or web interface?
- Performance issues (queries are slow, freezes at times, etc)
- no, runs smoothly
- Would they like help in administering the SCOP database?
- no
- What additional features or changes would users like to see?
- new tables or queries
- additional screens on application or web interface
- migrate to different database platform (i.e. MySQL to Oracle)
- none at the moment
