Using a triangular lattice model to study the designability of proteinfolding, we overcame the parity problem of previous cubic lattice model and enumerated all thesequences and compact structures on a simple two-dime...Using a triangular lattice model to study the designability of proteinfolding, we overcame the parity problem of previous cubic lattice model and enumerated all thesequences and compact structures on a simple two-dimensional triangular lattice model of size4+5+6+5+4. We used two types of amino acids, hydrophobic and polar, to make up the sequences, andachieved 2^(23)+2^(12) different sequences excluding the reverse symmetry sequences. The totalstring number of distinct compact structures was 219,093, excluding reflection symmetry in theself-avoiding path of length 24 triangular lattice model. Based on this model, we applied a fastsearch algorithm by constructing a cluster tree. The algorithm decreased the computation bycomputing the objective energy of non-leaf nodes. The parallel experiments proved that the fast treesearch algorithm yielded an exponential speed-up in the model of size 4+5+6+5+4. Designabilityanalysis was performed to understand the search result.展开更多
文摘Using a triangular lattice model to study the designability of proteinfolding, we overcame the parity problem of previous cubic lattice model and enumerated all thesequences and compact structures on a simple two-dimensional triangular lattice model of size4+5+6+5+4. We used two types of amino acids, hydrophobic and polar, to make up the sequences, andachieved 2^(23)+2^(12) different sequences excluding the reverse symmetry sequences. The totalstring number of distinct compact structures was 219,093, excluding reflection symmetry in theself-avoiding path of length 24 triangular lattice model. Based on this model, we applied a fastsearch algorithm by constructing a cluster tree. The algorithm decreased the computation bycomputing the objective energy of non-leaf nodes. The parallel experiments proved that the fast treesearch algorithm yielded an exponential speed-up in the model of size 4+5+6+5+4. Designabilityanalysis was performed to understand the search result.
