Comparison of the efficiency of evolutionary change-based and side chain orientation-based fold recognition potentials.
The present article describes residue level knowledge based potential SORDIS. SORDIS incorporates the information on side-chain orientation in relation to hydrophobic core centres, distance of residue from the globule centre and secondary structure. SORDIS has been tested and compared with widespread evolutionary change-based substitution matrices (BLOSUM, PAM, GONNET, Johnson-Overington, BLAJ, HSDM, and STROMA) in fold recognition experiments within the zone of weak sequence similarity (<16%). The obtained results show that the lower is the amino acid similarity between homologous pairs the higher is the performance of SORDIS in comparison with the potentials, based on the information about the evolutionary changes. Therefore, we propose that the employment of SORDIS in fold recognition can be useful.
Vishnepolsky
Boris
B
Institute of Molecular Biology and Biological Physics, Tbilisi 0160, Georgia.
Managadze
Grigol
G
Pirtskhalava
Malak
M
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D016208:Databases, Factual; D019143:Evolution, Molecular; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics
D011506:Proteins