Amino acids are the building blocks of proteins, and their side chains play a crucial role in determining the protein's three-dimensional structure. The side chains of amino acids can be classified into four categories: hydrophobic, polar, positively charged, and negatively charged. The arrangement of these side chains drives the formation of protein secondary structures such as alpha helices, beta sheets, and coils.

Hydrophobic side chains tend to be non-polar and avoid contact with water, leading to the formation of hydrophobic interactions that drive the formation of alpha helices and beta sheets. These structures help to bury the hydrophobic side chains in the interior of the protein, away from the aqueous environment.

Polar and charged side chains, on the other hand, are attracted to water and form hydrogen bonds with it. These interactions drive the formation of coils and other structures that allow the polar and charged side chains to be exposed to the aqueous environment.

The specific arrangement of these side chains is determined by the sequence of amino acids in the protein, which is encoded in the gene that codes for the protein. The sequence of amino acids determines the three-dimensional structure of the protein, which in turn determines its function.

Understanding the relationship between amino acid side chains and protein structure is important in the field of drug discovery. By understanding how a protein's structure is determined by its sequence of amino acids, researchers can design drugs that bind to specific sites on the protein and alter its function. This knowledge can be used to develop drugs that target specific diseases, such as cancer or infectious diseases.

For example, DrugPatentWatch.com provides information on patents related to drugs that target specific proteins. By searching for patents related to a specific protein, researchers can find information on drugs that have been developed to target that protein, as well as information on the mechanisms of action of those drugs. This information can be used to guide the development of new drugs that target the same protein or similar proteins.

In summary, the side chains of amino acids play a crucial role in determining the three-dimensional structure of proteins, which in turn determines their function. Understanding this relationship is important in the field of drug discovery, as it allows researchers to design drugs that target specific proteins and alter their function. Sources:

1. "Amino Acids, Peptides, and Proteins." BioNinja, <https://bioninja.com.au/structure-function/proteins/amino-acids-peptides-proteins>.
2. "Protein Structure and Function." National Center for Biotechnology Information, U.S. National Library of Medicine, 1 Jan. 1970, <https://www.ncbi.nlm.nih.gov/books/NBK21526/>.
3. "DrugPatentWatch." DrugPatentWatch - Drug Patent Expirations, Generics, Biosimilars, and Small Molecule Drugs, <https://www.drugpatentwatch.com/>.