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Rapidly Identify Therapeutic Proteins and Drug Targets

The immediate challenge of the genomics driven drug discovery process is to predict the precise biochemical function of the novel proteins needed to prioritize candidates for preclinical validation. The current solution relies on technologies for high-throughput sequence analysis and protein structure modeling to infer functional information. As demonstrated in the figure below, the existing approaches mainly classify the unknown protein to the level of protein superfamily and protein family, suggesting dubious functions. This level of functional annotation is not precise enough to properly choose the correct target, and in many instances incorrect protein leads are pursued wasting valuable resources and time. APT has developed a novel method that goes beyond the current capabilities of genomics companies allowing APT to assign precise biochemical function based on a knowledge of protein evolution, protein structure-function and enzyme mechanism and catalysis. This knowledge base, when combined with existing bioinformatics software, allows APT to distinguish the key differences among similar proteins, thus rapidly identifying the precise biochemical function of genes and the right therapeutic targets to pursue.

Selected Publications

1. J S. and Chen R. (2001). Functional misassignment of genes. Nature Biotechnology 19:95.
2. Chen R. (2001). Assigning precise function to genes. In Enzyme Technologies for Pharmaceutical and Biotechnological Application. Kirst HA, Yeh WK and Zmijewski MJ eds. Marcel Dekker, Inc. 537-554.
3. J S. and Chen R. (2000). Functional prediction: Identification of protein orthologs and paralogs. Protein Science 9: 2292-2301.