Folding algorithm

S Sun, PD Thomas, KA Dill. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng 8 769-778, 1995. 

Fig. 9. The transacetylase ribozyme. A Secondary structure of the clone 11 transacylase ribozyme based on the Zuker RNA folding algorithm Mfold. The oligonucleotide substrate is shaded in gray. The 2 -OH group of cytosine 147 (arrow) is the site of modification of the oligonucleotide substrate. B Reaction catalyzed by the clone 11 transacylase ribozyme. Note that the equilibrium of the reaction lies strongly on the side of the Bio-Phe-AMP substrate...

Pallansch, L., Beswick, H., Talian, J., and Zelenka, P. (1990) Use of an RNA folding algorithm to choose regions for amplification by the polymerase chain reaction. Anal. Biochem. 185, 57-62. 

Closure of hairpins of less than three nucleotides are not considered in the folding algorithm. 

The accuracy of the folding algorithm was tested on a database of structures that contains four small subunit ribosomal RNAs (rRNA), four Group I introns, three Group II introns, and 41 transfer RNAs (tRNA). The rRNAs and Group II introns were folded in domains of less than 500 nucleotides (5). Table III summarizes the percent of correctly predicted base pairs for this version of the algorithm and the last... 

It should be noted that a nontrivial aspect of making these comparisons is that the proteins were truncated differently in the various calculations we present all of the relevant information below so that the reader can draw his or her own conclusion. We do, however, wish to make one point with regard to the manner in which the comparison sequence is truncated. In our approach, truncation of terminal loop regions is done automatically using the secondary structure prediction, without reference to the native structure. In several of the comparisons we report below, truncation was carried out with the native structure in hand, presumably to minimize the RMSD obtained. While such results do indicate partial success of the folding algorithm, from a statistical... 

Units often have varying bit-widths. These bit-width mismatches create empty space within the sliced stack s bounding box. A stack folding algorithm folds small units into this empty space. After forming the sliced stacks, the rest of the random logic is placed around the stacks under constraints such as input/output port positions and aspect ratio. 

Use has been made of some of the above constraints in a test of a protein folding algorithm, as applied to BPTI (bovine pancreatic trypsin inhibitor). 

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