Substructures Identification

Three main spectra collections now exist. The first is the NIST/EPA/NIH mass spectral database, which contains 190 000 spectra of 163 000 compounds [1]. This original collection of spectra and related information is produced by the National Institute of Standards and Technology (NIST) with the assistance of expert advisors from the Environmental Protection Agency (EPA) and National Institutes of Health (NIH). This library is available on CD-ROM for personal computers with integrated tools for GC/MS deconvolution, mass spectra interpretation and chemical substructure identification. This US government publication is very cheap and of very high quality. This library is widely spread in many commercial mass spectrometers. Mass spectra for over 15 000 compounds are accessible on-line [2],... 

Some examples of codes for substructure identification are listed below. 

Hart, K. J., Palmer, P. T., Diedrich, D. L. and Enke, C. G. Generation of substructure identification rules using feature-combinations from tandem mass spectra. ]. Am. Soc. Mass Spectrom. 3 159-168, 1992. 

Thiostrepton derivatives, 156/ structure-based antibiotic design Amide coupling, 156 binding to L11BD, 155 docking of structures, 155 substructure identification, 155-156 Thiostrepton- and Micrococin-binding models, 155... 

Koh, C. G. and Shankar, K. Substructural identification method without interface measurement. Journal of Engineering Mechanics (ASCE) 129(7) (2003), 769-776. 

Yuen, K.-V. and Katafygiotis, L. Substructure identification and health monitoring using response measurement only. Computer-Aided Civil and Irfrastructure Engineering 21(4) (2006), 280-291. 

Stein, S.E. (1995) Chemical substructure identification by mass spectral library searching. /. Am. 

Kalman RE, Bucy R (1961) New results in linear filtering and prediction theory. J Basic Eng 83 95-108 Katafygiotis LS, Beck JL (1998) Updating models and their uncertainties. II model identifiability. J Eng Mech (ASCE) 124(4) 463 67 Koh CG, Shankar K (2003) Substructural identification method without interface measurement. J Eng Mech (ASCE) 129(7) 769-776... 

A substructure search algorithm is usually the first step in the implementation of other important topological procedures for the analysis of chemical structures such as identification of equivalent atoms, determination of maximal common substructure, ring detection, calculation of topological indices, etc. 

Burden, F. R. Molecular identification number for substructure searches. 

We are developing an expert system to automate the first step of this process, the interpretation of molecular spectra and identification of substructures present in the molecule. The automatic interpretation of spectra would by itself provide a useful tool for an organic chemist who may not be an expert spectroscopist. Also, reported algorithms for the assembly of candidate structures from known substructures, such as the GENOA program. (3-6) rely on the input of accurate and specific substructures in order to function correctly and efficiently. Identification of substructures is thus a logical starting point. 

Gillet, V. J., Willett, R, and Bradshaw, J. (1998) Identification of biological activity profiles using substructural analysis and genetic algorithms. J. Chem. Inf. Comput. Sci. 38, 165-179. 

Like the similarity protocol, the user interface for the Pipeline Pilot SSS protocol supports multiple databases and multiple probes in a single query. The input of the probe molecule(s) is accomplished using a SD file, which can be generated in most standard chemical drawing programs. This file is supplied as one of the inputs in the SSS interface. The use of identification numbers is not as applicable here as it is in the case of the similarity protocol since we are most likely not using existing molecules as substructures. Consequently, textbox input is not an option nor is the upload of a list of numbers in CSV or Excel format. 

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