Fast Tree Search for A Triangular Lattice Model of Protein Folding
- Author:
Li XIAOMEI
1
;
Wang NENGCHAO
Author Information
1. 华中科技大学
- Keywords:
triangular lattice model;
protein folding;
fast search tree;
designability
- From:
Genomics, Proteomics & Bioinformatics
2004;2(4):245-252
- CountryChina
- Language:Chinese
-
Abstract:
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 223+212 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.
