Homology Modeling

Homology Modeling. Another common challenge in CADD research is determining the 3-D structure of proteins. Most drug targets are proteins, so it’s important to know their 3-D structure in detail. It’s estimated that the human body has 500,000 to 1 million proteins. However, the 3-D structure is known for only a small fraction of these. Homology modeling is one method used to predict 3-D structure. In homology modeling, the amino acid sequence of a specific protein (target) is known, and the 3-D structures of proteins related to the target (templates) are known. Bioinformatics software tools are then used to predict the 3-D structure of the target based on the known 3-D structures of the templates. MODELLER is a well-known tool in homology modeling, and the SWISS-MODEL Repository is a database of protein structures created with homology modeling.

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Virtual High-Throughput Screening (vHTS)

Virtual High-Throughput Screening (vHTS). Pharmaceutical companies are always searching for new leads to develop into drug compounds. One search method is virtual high-throughput screening. In vHTS, protein targets are screened against databases of small-molecule compounds to see which molecules bind strongly to the target. If there is a “hit” with a particular compound, it can be extracted from the database for further testing. With today’s computational resources, several million compounds can be screened in a few days on sufficiently large clustered computers. Pursuing a handful of promising leads for further development can save researchers considerable time and expense. ZINC is a good example of a vHTS compound library.

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