JChem Base

chemical interface to relational database engines

JChem Base is a tool for the development of cheminformatics applications allowing storage and search of structural and non-structural data. JChem Base can handle molecule, reaction, polymer, Markush and query structural contents. JChem Base will integrate with a variety of database systems (Oracle, MS SQL Server, DB2, Access, etc) with web interfaces and offers fast substructure, similarity, exact, superstructure and other searches.

General overview

Structures are stored in database tables, combining structural and non-structural data. SDF, SMILES, MOL, RDF, CML, and many other file formats are supported. JChem Base also supports ChemAxon’s Chemical Terms language to enable complex chemical queries, expressions and rules. The system includes Marvin, a suite of chemical editor, viewer and visualization tools and graphical user interfaces. Markush Search add-on allows the registration of generic structures into the database and substructure, full structure and duplicate searching in enumerated libraries without enumeration of library members. Learn more about Markush Search add-on »

Base features

  • Sophisticated and efficient search algorithm
  • Automatically calculated Chemical Terms columns
  • Standardizer integration
  • Ready-to-use example web applications using Marvin Applets are included in the distribution
JChem manager GUI

Advanced features

  • full structure, substructure, superstructure and duplicate matching
  • variable similarity searching including reaction similarity
  • registration and searching of polymers, mixtures and formulations
  • generic query atoms
  • various query properties supported
  • full SMARTS support including recursive SMARTS
  • R-group query expressions
  • reaction queries, including reaction mapping, reaction query features
  • stereo specific structure and reaction specifications
  • structure canonicalization
  • chemical terms support
  • different types of tautomer search
  • extensive search options

Articles in the library

JChem Engines

May 10, 2017 - Presentation
ChemAxon’s search and database technology includes our JChem Base tool and two cartridges: One running on Oracle, and the other on PostgreSQL. We usually refer to these products as the …

Efficient Heuristics for Maximum Common Substructure Search

Apr 11, 2015 - Publication
Maximum common substructure search is a computationally hard optimization problem with diverse applications in the field of cheminformatics, including similarity search, lead optimization…

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