Search for the most stable folds of protein chains: III. Improvement in fold recognition by averaging over homologous sequences and 3D structures.
Three-dimensional (3D) protein fold recognition by query sequence can be improved using information of fold recognition yielded by the sequences homologous to the query one. This idea is now used more and more widely. Our paper presents its consequent development. We suggest incorporating information both on the sequences homologous to the query protein sequence and the 3D structures homologous to the target (already deciphered) protein folds. We show that both these tricks, and especially their combination reduces errors in fold recognition by the threading method. Proteins 2000;40:494-501.
Rykunov
D S
DS
Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
Lobanov
M Y
MY
Finkelstein
A V
AV
D000596:Amino Acids / Q000737:chemistry; D003198:Computer Simulation; D005544:Forecasting; D008956:Models, Chemical; D008958:Models, Molecular; D010363:Pattern Recognition, Automated; D017510:Protein Folding; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics
D000596:Amino Acids