Name
Abstract | ||
|---|---|---|
Previous study shows that the same type of bond lengths and angles fit Gaussian distributions well with small standard deviations on high resolution protein structure data. The mean values of these Gaussian distributions have been widely used as ideal bond lengths and angles in bioinformatics. However, we are not aware of any research work done to evaluate how accurately we can model protein structures with dihedral angles and ideal bond lengths and angles. In this paper, we first introduce the protein structure idealization problem. Then, we develop a fast O(nm / ε) dynamic programming algorithm to find an approximately optimal idealized protein backbone structure according to our scoring function. Consequently, we demonstrate that idealized backbone structures always exist with small changes and significantly better free energy. We also apply our algorithm to refine protein pseudo-structures determined in NMR experiments. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1007/978-3-642-33122-0_22 | WABI |
Keywords | Field | DocType |
idealized backbone structure,high resolution protein structure,bond length,protein structure,optimal idealized protein backbone,gaussian distribution,ideal bond length,protein structure idealization problem,dihedral angle,small change,dynamic programming algorithm,model protein structure | Dynamic programming,Graphical models for protein structure,Combinatorics,Bond length,Gaussian,Peptide bond,Standard deviation,Dihedral angle,Mathematics,Protein structure | Conference |
Citations | PageRank | References |
0 | 0.34 | 5 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Xuefeng Cui | 1 | 24 | 5.98 |
| Shuai Cheng Li | 2 | 184 | 30.25 |
| Dongbo Bu | 3 | 157 | 21.54 |
| Babak Alipanahi Ramandi | 4 | 0 | 0.34 |
| Ming Li | 5 | 5595 | 829.00 |