Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?

ABSTRACT: : Previous studies show 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 done to evaluate how accurately we can model protein structures with dihedral angles and ideal bond lengths and angles.Here, we introduce the protein structure idealization problem. We focus on the protein backbone structure idealization. We describe a fast O(nm/ε) dynamic programming algorithm to find an idealized protein backbone structure that is approximately optimal according to our scoring function. The scoring function evaluates not only the free en

SUBMITTER: Cui X 

PROVIDER: S-EPMC3655034 | biostudies-literature | 2013 Feb

REPOSITORIES: biostudies-literature