Tertiary protein structure simulations

Now, several software programs can be used to examine the secondary structure of proteins in the protein databank. In addition, computer simulation is being developed to visualize the secondary and tertiary structure of proteins, which occur within microseconds of the formation of the primary structure. These computer simulations are bound to provide a better insight into the protein structure and perhaps establish the rules of secondary and tertiary structure formations. 

S. Sun, Reduced representation approach to protein tertiary structure prediction statistical potential and simulated annealing, J. Theor. Biol. 172 (1995), 13-32. 

Figure 7-16. Superimpasition of the X-ray structure of the tetracycline repressor class D dimer (dark, protein database entry 2TRT) with the calculated geometrical average of a 3 ns MD simulation (light trace). Only the protein backbone C trace Is shown, The secondary structure elements and the tertiary structure are almost perfectly reproduced and maintained throughout the whole production phase of the calculation,...

Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997 268 209-25. 

H. Kawai, T. Kikuchi, and Y. Okamoto, Protein Engin., 3, 85 (1989). A Prediction of Tertiary Structures of Peptide by the Monte Carlo Simulated Annealing Method. 

A tool of computational chemistry, simulated annealing, is now almost a routine part of solving the tertiary structure of a protein. Also plotted in Figure 16 is the trend of CJACS mentions of a program for simulated annealing, X-PLOR, which is widely used by crystallographers. It is clear that growth in use of the Protein Data Bank and the use of X-PLOR have been nearly parallel since 1989. 

J. Skolnick and A. Kolinski, Computer Simulations of Globular Protein Folding and Tertiary Structure, Annu. Rev. Phys. Chem., 40 (1989) 207. 

The feedback-optimized parallel tempering technique [26] outlined in the previous section has recently been applied to study the folding of the 36-residue chicken villin headpiece sub-domain HP-36 [27]. Since HP-36 is one of the smallest proteins with well-defined secondary and tertiary structure [28] and at the same time with 596 atoms still accessible to numerical simulations, it has recently attracted considerable interest as an example to test novel numerical techniques, including molecular dynamics [29,30] and Monte Carlo [31,32] methods. The experimentally determined structure [28] which is deposited in the Protein Data Bank (PDB code Ivii) is illustrated in the left panel of Fig. 6. 

Ortiz, A. R., A. Kolinski, and J. Skolnick, Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. Proteins, 1998. 30(3) p. 287-94. 

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