Defining topological equivalences in protein structures by means of a dynamic programming algorithm.
An automatic algorithm for defining topological equivalences in protein structures is presented. The algorithm is based on a dynamic programming technique and self-consistent scoring method. We have used it to align pairs of similar protein structures of several protein families and to identify recurrent structural domains in aspartic proteinase 2APR. Its ability to find suboptimal paths permits a thorough comparison of proteins at each level in the hierarchy of the protein structure: secondary structure, super-secondary structure, domain and entire globular structure. The algorithm has been extended to the structure alignment of ribonucleic acid and can be extended to the structure alignment of any linear polymer.
Luo
Y
Y
Department of Chemistry, Peking University, Beijing, PRC.
Lai
L
L
Xu
X
X
Tang
Y
Y
D000465:Algorithms; D016282:Aspartic Acid Endopeptidases / Q000737:chemistry; D001665:Binding Sites; D010446:Peptide Fragments / Q000737:chemistry; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
D010446:Peptide Fragments; D011506:Proteins; D016282:Aspartic Acid Endopeptidases