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Posted 09.13.04

New Database Speeds Retrieval of Protein Structures

MU Researcher's New Protein Database Will Improve Development Time for Life-Saving Medication

COLUMBIA, Mo. -- A Web search utilizing engines such as Yahoo and Google can potentially produce thousands of results in less than a second. University of Missouri-Columbia researchers have developed a similar database search engine that will accelerate and improve the process and development of new protein-based drugs that combat diseases such as cancer and AIDS. The database is featured in the Sept. 3 edition of Science.

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The database consists of more than 50,000 3D chains of protein structures. These 3-D structures are critical to understanding the function of proteins in cells and how they interact with drugs. This knowledge can help researchers see how particular mutations or variations in genes that encode a particular protein lead to changes in the protein's behavior, which can result in disease or explain differences in a person's reaction to certain drugs.

"This search engine is the world's first and only real-time 3-D protein structure retrieval system," said Chi-Ren Shyu, assistant professor of computer science engineering at MU. "The system, called ProteinDBS, can provide researchers with high retrieval accuracy and an efficient search from a complete protein tertiary structure database."

Before ProteinDBS was developed, Shyu said, it would take hours for researchers to retrieve protein structures from databases for short queries and days for long queries. ProteinDBS allows people to enter a protein structure or a Protein Databank ID number and retrieves the most similar database structures that researchers have studied.

The ProteinDBS search produces in seconds the 50 proteins that most resemble the search subject and allows for visual and statistical comparisons. For example, Shyu said, someone could superimpose 3-D portraits of two proteins or examine their sequences by individual amino acids.

"ProteinDBS's unique ability to perform real-time structure comparison will invite substantially more scientists to partake in protein structure analysis in life science research," Shyu said.

Shyu's database, which also was featured in the July edition of Nucleic Acids Research, can be accessed at


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