Paper Info
Title
Automatic Determination of Reaction Mappings and Reaction Center Information. 2. Validation on a Biochemical Reaction Database.
Abstract
The correct identification of the reacting bonds and atoms is a prerequisite for the analysis of the reaction mechanism. We have recently developed a method based on the Imaginary Transition State Energy Minimization approach for automatically determining the reaction center information and the atom-atom mapping numbers. We test here the accuracy of this ITSE approach by comparing the predictions of the method against more than 1500 manually annotated reactions from BioPath, a comprehensive database of biochemical reactions. The results show high agreement between manually annotated mappings and computational predictions (98.4%), with significant discrepancies in only 24 cases out of 1542 (1.6%). This result validates both the computational prediction and the database, at the same time, as the results of the former agree with expert knowledge and the latter appears largely self-consistent, and consistent with a simple principle. In 10 of the discrepant cases, simple chemical arguments or independent literature studies support the predicted reaction center. In five reaction instances the differences in the automatically and manually annotated mappings are described in detail. Finally, in approximately 200 cases the algorithm finds alternate reaction centers, which need to be studied on a case by case basis, as the exact choice of the alternative may depend on the enzyme catalyzing the reaction.
Year
DOI
Venue
2008
10.1021/ci700433d
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Keywords
Field
DocType
reaction center
Data mining,Computer science,Biochemical reactions,Bioinformatics,Database,Energy minimization,Reaction mechanism
Journal
Volume
Issue
ISSN
48
6
1549-9596
Citations 
PageRank 
References 
10
0.71
0
Authors
4
Name
Order
Citations
PageRank
Joannis Apostolakis11129.64
Oliver Sacher2263.08
Robert Körner3554.83
Johann Gasteiger453085.24