Name
Title | ||
|---|---|---|
A quasi-physical algorithm for the structure optimization in an off-lattice protein model. |
Abstract | ||
|---|---|---|
In this paper, we study an off-lattice protein AB model with two species of monomers, hydrophobic and hydrophilic, and present a heuristic quasi-physical algorithm. First, by elaborately simulating the movement of the smooth solids in the physical world, we find low-energy conformations for a given monomer chain. A subsequent off-trap strategy is then proposed to trigger a jump for a stuck situation in order to get out of the local minima. The algorithm has been tested in the three-dimensional AB model for all sequences with lengths of 13-55 monomers. In several cases, we renew the putative ground state energy values. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. |
Year | DOI | Venue |
|---|---|---|
2006 | 10.1016/S1672-0229(06)60018-1 | Genomics, Proteomics & Bioinformatics |
Keywords | Field | DocType |
protein folding,off-lattice model,quasi-physical algorithm,off-trap strategy | Heuristic,Protein folding,Ground state,Biology,Algorithm,Maxima and minima,Lattice protein,Jump,Monomer,Protein structure | Journal |
Volume | Issue | ISSN |
4 | 1 | 1672-0229 |
Citations | PageRank | References |
0 | 0.34 | 2 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Jingfa Liu | 1 | 98 | 12.48 |
| Wenqi Huang | 2 | 399 | 24.25 |
| wenqi | 3 | 0 | 0.34 |
| huang | 4 | 0 | 0.68 |