Secondary structure computational

Hanke, J. Reich, J. G. (1996). Kohonen map as a visualization tool for the analysis of protein sequences multiple alignments, domains and segments of secondary structures. Comput Applic Biosci 6,447-54. 

Many plastic products seen in everyday life are not required to undergo sophisticated design analysis because they are not required to withstand extreme loading conditions such as creep and fatigue loads. Examples include containers cups toys boxes housings for computers, radios, televisions and the like and nonstructural or secondary structural products of various kinds in buildings, aircraft, appliances, and electronic devices. These type products require reviewing... 

This branch of bioinformatics is concerned with computational approaches to predict and analyse the spatial structure of proteins and nucleic acids. Whereas in many cases the primary sequence uniquely specifies the 3D structure, the specific rules are not well understood, and the protein folding problem remains largely unsolved. Some aspects of protein structure can already be predicted from amino acid content. Secondary structure can be deduced from the primary sequence with statistics or neural networks. When using a multiple sequence alignment, secondary structure can be predicted with an accuracy above 70%. 

Each protein has a unique three-dimensional shape called its tertiary structure. The tertiary structure is the result of the bends and folds that a polypeptide chain adopts to achieve the most stable structure for the protein. As an analogy, consider the cord in Figure 13-39 that connects a computer to its keyboard. The cord can be pulled out so that it is long and straight this corresponds to its primary structure. The cord has a helical region in its center this is its secondary structure. In addition, the helix may be twisted and folded on top of itself This three-dimensional character of the cord is its tertiary structure. 

Molecular dynamics simulations are capable of addressing the self-assembly process at a rudimentary, but often impressive, level. These calculations can be used to study the secondary structure (and some tertiary structure) of large complex molecules. Present computers and codes can handle massive calculations but cannot eliminate concerns that boundary conditions may affect the result. Eventually, continued improvements in computer hardware will provide this added capacity in serial computers development of parallel computer codes is likely to accomplish the goal more quickly. In addition, the development of realistic, time-efficient potentials will accelerate the useful application of dynamic simulation to the self-assembly process. In addition, principles are needed to guide the selec-... 

The endoxylanase gene from Thermoanaerobacter strain B6A was sequenced and structural interpretations were deduced from computer analysis of the amino acid sequence (see Table VIII). The endoglucanase is hydrophilic and has compact secondary structure with 30 6-tums and five potential glycosylation sites. 

Rost, B., Sander, C., and Schneider, R. (1994) PHD—an automatic mail server for protein secondary structure prediction. Comput. Appl. Biosci. 10, 53-60. 

RPC of small peptides can also be used for peptide identification, based on their amino acid composition. Computer programs able to predict peptide retention time are available, thus simplifying peptide identihcation. These programs generally work well with peptide up to 20 amino acids, but fail with larger peptides for which the secondary structure may contribute signihcantly to the retention. 

Perczel, A., Jakli, I., Csizmadia, I.G. (2003). Intrinsically stable secondary structure elements of proteins A comprehensive study of folding units of proteins by computation and by analysis of data determined by x-ray crystallography. Chemistry, 9(21), 5332-5342. 

A puzzling problem was posed by Levinthal many years ago.329 We usually assume that the peptide chain folds into one of the most stable conformations possible. However, proteins fold very rapidly. Even today, no computer would be able, in our lifetime, to find by systematic examination the thermodynamically most stable conformation.328 It would likewise be impossible for a folding protein to "try out" more than a tiny fraction of all possible conformations. Yet folded and unfolded proteins often appear to be in a thermodynamic equilibrium Experimental results indicate that denatured proteins are frequently in equilibrium with a compact denatured state or "molten globule" in which hydrophobic groups have become clustered and some secondary structures exists.330-336 From this state the polypeptide may rearrange more slowly through other folding intermediates to the final "native conformation."3363 3361 ... 

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