Layers: A molecular surface peeling algorithm and its applications to analyze protein structures.

ABSTRACT: We present an algorithm 'Layers' to peel the atoms of proteins as layers. Using Layers we show an efficient way to transform protein structures into 2D pattern, named residue transition pattern (RTP), which is independent of molecular orientations. RTP explains the folding patterns of proteins and hence identification of similarity between proteins is simple and reliable using RTP than with the standard sequence or structure based methods. Moreover, Layers generates a fine-tunable coarse model for the molecular surface by using non-random sampling. The coarse model can be used for shape comparison, protein recognition and ligand design. Additionally, Layers can be used to develop biased initial configuration of molecules for protein folding simulations. We have developed a random forest cl

SUBMITTER: Karampudi NB 

PROVIDER: S-EPMC4639851 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature