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Fast tree search for enumeration of a lattice model of protein folding

By Henry Cejtin, Jan Edler, Allan Gottlieb, Robert Helling, Hao Li, James Philbin, Chao Tang and Ned Wingreen

Abstract

Using a fast tree-searching algorithm and a Pentium cluster, we enumerated all the sequences and compact conformations (structures) for a protein folding model on a cubic lattice of size 4 × 3 × 3. We used two types of amino acids – hydrophobic (H) and polar (P) – to make up the sequences, so there were 2 36 ≈ 6.87 ×10 10 different sequences. The total number of distinct structures was 84,731,192. We made use of a simple solvation model in which the energy of a sequence folded into a structure is minus the number of hydrophobic amino acids in the “core ” of the structure. For every sequence, we found its ground state or ground states, i.e., the structure or structures for which its energy is lowest. About 0.3 % of the sequences have a unique ground state. The number of structures that are unique ground states of at least one sequence is 2,662,050, about 3 % of the total number of structures. However, these “designable ” structures differ drastically in their designability, defined as the number of sequences whose unique ground state is that structure. To understand this variation in designability, we studied the distribution of struc

Year: 2002
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