Biocomputing and Media Research Lab

Image: Figures pertaining to research

Molecular Query Retrieval


Discerning the similarity between two molecules is a challenging problem in molecular biology as well as in drug discovery. Since similar molecules often have similar biological behaviors and chemical properties, molecular similarity is a key notion in biochemical investigations targeted at understanding existing molecules as well as guiding the synthesis of new molecules. Additionally, molecular similarity plays a key-role in structure-based query-retrieval in molecular databases as well as in computational investigations seeking to understand the structural space.
Our research in this area targets both large molecules, such as proteins and enzymes, and small pharmaceutically relevant molecules. Our current investigations focus on different aspects of this problem including: designing novel molecular representations that have high bio-chemical relevance, designing non-linear matching metrics, and designing algorithms that allow molecular comparisons in real-time on very-large molecular repositories using complex molecular representations. Results from this project are also used in the FreeFlowDB project.
This research is funded by the National Science Foundation grant IIS-0644418 and the California State University Program for Education and Research in Biotechnology (CSUPERB).


  1. R. Singh, Surface Similarity-Based Molecular Query-Retrieval, BMC Cell-Biology, Vol. 8, Suppl.1 (S6): July, 2007. [PDF]
  2. E. Velasquez, E. R. Yera, and R. Singh, "Determining Molecular Similarity for Drug Discovery using the Wavelet Riemannian Metric", IEEE Symposium on Bioinformatics and Bioengineering (BIBE), pp. 261-268, 2006. [PDF]
  3. R. Singh, "Molecular Informatics and Image Analysis", Workshop on Multiscale Biological Imaging, Data Mining, and Informatics, pp. 47-48, 2006. [PDF]
  4. R. Singh, "A Computer Vision-Based Approach for Answering Molecular Similarity Queries", Proc. Asian Conference on Computer Vision (ACCV), 2004. [PDF]
  5. R. Singh, "Reasoning About Molecular Similarity and Properties", Proc. IEEE Computational Systems Bioinformatics Conference (CSB), 2004. [PDF]
  6. R. Singh, "Issues in Computational Modeling of Molecular Structure-Property Relationships in Real-World Settings", Proc. Conference on Systemics, Cybernetics, and Informatics (SCI), Vol. VII, pp. 63-68, 2004. [PDF]
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