CHORD

CHORD is Chemical Objects in a Relational Database. It uses cartridge technology to allow you to fully integrate chemical structures with data. CHORD easily handles database tables containing many millions of structures. CHORD provides the ability to:

• perform fast sub-structure searching or more complex SMARTS matching.
• convert to and from molecular file formats.
• create and interpret chemical names.
• carry out reaction transformations.
• perform similarity searching and measurement.
• make unique SMILES strings to facilitate structure lookup.
• compute fingerprints to pre-screen structures and speed sub-structure searches.

CHORD offers unique capabilities not found in other database cartridges. From within the database, you can compute fragment-based properties, such as polar surface area, and fragment-key fingerprints. This allows you to define your own fragments to compute other properties or produce novel fingerprints. This capability makes CHORD especially well suited for applications that combine computational chemistry calculations with other types of data analysis and searching.

CHORD is built around PostgreSQL, a professional, easy to use and free relational database system. For chemical searching, CHORD integrates OpenEye’s OEChem, a complete, fast and powerful function library. OpenEye is famous for its 3D structure capabilities. Watch for future releases of CHORD to include integration of 3D structures and searching!

With so many excellent cheminformatics tools available, integration has become an important consideration in modern software development. CHORD plays well with others and can be used in many ways, for example:

• a SQL engine for your web applications combining structure and chemical or biological data searching.
• a research tool for developing new fragment-based property calculations or fingerprints.
• a teaching tool for cheminformatics.

Be sure to check out the demos link above, to see some simple examples of what could be done with CHORD.

makefp

makefp is a command line program that creates path-based fingerprints from input SMILES, or other structure file, such as SDF.

Platforms

CHORD and makefp have been thoroughly tested on these platforms. Please contact us at info@gnova.com if you need support on other platforms. We're considering other Linux distributions, and will take our cue from you. Tell us what you need! We also routinely use VMWare Workstation running Linux on a Windows XP host - very slick and highly affordable.

*RedHat Enterprise 4,5; Ubuntu 7.10; SUSE 10 inquire about others
^†PostgreSQL 8.1, 8.2
^‡OEChem 1.4, 1.5