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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References
A comprehensive set of sequence analysis programs for the VAX
TL;DR: A group of programs that will interact with each other has been developed for the Digital Equipment Corporation VAX computer using the VMS operating system.
A general method applicable to the search for similarities in the amino acid sequence of two proteins
TL;DR: A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed and it is possible to determine whether significant homology exists between the proteins to trace their possible evolutionary development.
13.2K
The Protein Data Bank: a computer-based archival file for macromolecular structures.
Frances C. Bernstein,Thomas F. Koetzle,Graheme J. B. Williams,Edgar F. Meyer,Michael D. Brice,John R. Rodgers,O. Kennard,Takehiko Shimanouchi,Mitsuo Tasumi +8 more
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.
8.7K
•Book
Atlas of protein sequence and structure
M. A. Chang,M. O. Dayhoff,R. V. Eck,M. R. Sochard +3 more
- 01 Jan 1965
The interpretation of protein structures: estimation of static accessibility.
B. Lee,Frederic M. Richards +1 more
TL;DR: The accessibility of atoms in the twenty common amino acids in model tripeptides of the type Ala-X-Ala are given for defined conformation and the larger non-polar amino acids tend to be more “buried” in the native form of all three proteins.
6K