Patent10.1126/SCIENCE.1853201
Method to identify protein sequences that fold into a known three-dimensional structure
TL;DR: In this article, a computer-assisted method for identifying protein sequences that fold into a known 3D structure was proposed, based on three key features of each residue's environment within the structure: (1) the total area of the residue's side-chain that is buried by other protein atoms, inaccessible to solvent; (2) the fraction of the side-chains area that is covered by polar atoms (O, N) or water; and (3) the local secondary structure.
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Abstract: A computer-assisted method for identifying protein sequences that fold into a known three-dimensional structure. The method determines three key features of each residue's environment within the structure: (1) the total area of the residue's side-chain that is buried by other protein atoms, inaccessible to solvent; (2) the fraction of the side-chain area that is covered by polar atoms (O, N) or water, and (3) the local secondary structure. Based on these parameters, each residue position is categorized into an environment class. In this manner, a three-dimensional protein structure is converted into a one-dimensional environment string. A 3D structure profile table is then created containing score values that represent the frequency of finding any of the 20 common amino acids structures at each position of the environment string. These frequencies are determined from a database of known protein structures and aligned sequences.
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