An algorithm for prediction of structural elements in small proteins.
A method for predicting the location of surface loops/turns and assigning the intervening secondary structure of the transglobular linkers in small, single domain globular proteins has been developed. Application to a set of 10 proteins of known structure indicates a high level of accuracy. The secondary structure assignment in the center of transglobular connections is correct in more than 85% of the cases. A similar error rate is found for loops. Since more global information about the fold is provided, it is complementary to standard secondary structure prediction approaches. Consequently, it may be useful in early stages of tertiary structure prediction when establishment of the structural class and possible folding topologies is of interest.
Kolinski
A
A
Scripps Research Institute, Department of Molecular Biology, La Jolla, California 92037, USA. kolinski@chem.uw.edu.pl
Skolnick
J
J
Godzik
A
A
D000465:Algorithms; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry; D019295:Computational Biology; D003198:Computer Simulation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D016415:Sequence Alignment
D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D011506:Proteins