New method for protein secondary structure assignment based on a simple topological descriptor.
A simple, five-element descriptor, derived from the Delaunay tessellation of a protein structure in a single point per residue representation, can be assigned to each residue in the protein. The descriptor characterizes main-chain topology and connectivity in the neighborhood of the residue and does not explicitly depend on putative hydrogen bonds or any geometric parameter, including bond length, angles, and areas. Rules based on this descriptor can be used for accurate, robust, and computationally efficient secondary structure assignment that correlates well with the existing methods.
Taylor
Todd
T
Laboratory for Structural Bioinformatics, School of Computational Sciences, George Mason University, Manassas, Virginia 20110, USA.
Rivera
Margarita
M
Wilson
Glenda
G
Vaisman
Iosif I
II
D000465:Algorithms; D000595:Amino Acid Sequence; D055592:Biophysical Phenomena; D001703:Biophysics; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012680:Sensitivity and Specificity; D012984:Software; D040681:Structural Homology, Protein
D011506:Proteins