Improved algorithms for quantifying the near symmetry of proteins: complete side chains analysis.

ABSTRACT: Symmetry of proteins, an important source of their elegant structure and unique functions, is not as perfect as it may seem. In the framework of continuous symmetry, in which symmetry is no longer a binary yes/no property, such imperfections can be quantified and used as a global descriptor of the three-dimensional structure. We present an improved algorithm for calculating the continuous symmetry measure for proteins that takes into account their complete set of atoms including all side chains. Our method takes advantage of the protein sequence and the division into peptides in order to improve the accuracy and efficiency of the calculation over previous methods. The Hungarian algorithm is applied to solve the assignment problem and find the permutation that defines the symmetry operation

SUBMITTER: Tuvi-Arad I 

PROVIDER: S-EPMC6551912 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature