Modular Chemical Descriptor Language (MCDL): Stereochemical modules

Journal Article · Sat Jan 01 04:00:00 EST 2011 · Journal of Cheminformatics

DOI:https://doi.org/10.1186/1758-2946-3-5· OSTI ID:1018239

Gakh, Andrei A ^[1]; Burnett, Michael N ^[1]; Trepalin, Sergei V. ^[2]; Yarkov, Alexander V ^[2]

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1. ORNL
2. Institute Physiologically Active Compouds, Russian Academy of Sciences, Moscow

In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDL processing module software packages. Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: NNSA USDOE - National Nuclear Security Administration (NNSA)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 1018239
• Journal Information: Journal of Cheminformatics, Journal Name: Journal of Cheminformatics Journal Issue: 1 Vol. 3; ISSN 1758-2946
• Country of Publication: United States
• Language: English

Related Subjects

99 GENERAL AND MISCELLANEOUS
ALGORITHMS
ISOMERS
JAVA
PERFORMANCE
PROCESSING
STEREOCHEMISTRY
STORAGE
TESTING