Related Experiment Video
Updated: Nov 2, 2025

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
Published on: June 17, 2012
Predicting biological pathways of chemical compounds with a profile-inspired approach
Javier Lopez-Ibañez1, Florencio Pazos1, Monica Chagoyen2
1Computational Systems Biology Group, National Center for Biotecnology (CNB-CSIC), Darwin 3, 28049, Madrid, Spain.
Background:
Assignment of chemical compounds to biological pathways is a crucial step to understand the relationship between the chemical repertory of an organism and its biology. Protein sequence profiles are very successful in capturing the main structural and functional features of a protein family, and can be used to assign new members to it based on matching of their sequences against these profiles. In this work, we extend this idea to chemical compounds, constructing a profile-inspired model for a set of related metabolites (those in the same biological pathway), based on a fragment-based vectorial representation of their chemical structures.
Results:
We use this representation to predict the biological pathway of a chemical compound with good overall accuracy (AUC 0.74-0.90 depending on the database tested), and analyzed some factors that affect performance. The approach, which is compared with equivalent methods, can in addition detect those molecular fragments characteristic of a pathway.
Conclusions:
The method is available as a graphical interactive web server http://csbg.cnb.csic.es/iFragMent .
More Related Videos
Related Concept Videos
Drug Discovery: Overview
Structure-Activity Relationships and Drug Design
SAR studies the intricate relationship between a drug's chemical structure and biological activity. It focuses on understanding how modifications to a drug's structure can influence...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces
Predicting Reaction Outcomes

