Fast tree search for a triangular lattice model of protein folding.
Using a triangular lattice model to study the designability of protein folding, we overcame the parity problem of previous cubic lattice model and enumerated all the sequences and compact structures on a simple two-dimensional triangular lattice model of size 4+5+6+5+4. We used two types of amino acids, hydrophobic and polar, to make up the sequences, and achieved 2(23)+2(12) different sequences excluding the reverse symmetry sequences. The total string number of distinct compact structures was 219,093, excluding reflection symmetry in the self-avoiding path of length 24 triangular lattice model. Based on this model, we applied a fast search algorithm by constructing a cluster tree. The algorithm decreased the computation by computing the objective energy of non-leaf nodes. The parallel experiments proved that the fast tree search algorithm yielded an exponential speed-up in the model of size 4+5+6+5+4. Designability analysis was performed to understand the search result.
Li
Xiaomei
X
Computer Science and Technology Institute, Huazhong University of Science and Technology, Wuhan 430074, China. lxmdwj@163.com
Wang
Nengchao
N
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology; D008958:Models, Molecular; D015233:Models, Statistical; D017510:Protein Folding; D013816:Thermodynamics
D000596:Amino Acids