SIMULATION OF α-HELIX AND β-HAIRPIN FORMATION IN WATER-SOLUBLE PROTEINS BY THE CODE PHYSICS METHOD
B. V. Shestopalov
Institute of Cytology RAS, St. Petersburg;
e-mail: shest@mail.cytspb.rssi.ru
One of the possible ways for complete and final solution of the problem of determination of three-dimensional
structure of proteins on amino acid sequence is simulation of protein three-dimensional structure formation.
The use of the code physics method developed by the author has been suggested to fulfill this task. The simulation
of α-helix and β-hairpin formation in water-soluble proteins as a start of realization of the plan is
described here. The results of the simulation were compared with the experimental data for 14 proteins of no more
than 50 amino acids and therefore with little number of α-helices and β-strands (to meet limits of
simulation process) and with secondary structure predictions by the best to data methods of protein secondary
strunture prediction, PSIpred, PORTER and PROFsec. Secondary structure of the proteins, obtained as a result of the
simulation of α-helix and β-hairpin formation using the code physics method, corresponded completely to
experimental data while the secondary structure predicted by the PSIpred, PORTER and PROFsec methods differed from
these data significantly.
Key words: physics, encoding, simulation, protein three-dimensional structure, α-helix,
β-structure
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