SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information.

ABSTRACT: In this paper, we describe SAFlex (Structural Alphabet Flexibility), an extension of an existing structural alphabet (HMM-SA), to better explore increasing protein three dimensional structure information by encoding conformations of proteins in case of missing residues or uncertainties. An SA aims to reduce three dimensional conformations of proteins as well as their analysis and comparison complexity by simplifying any conformation in a series of structural letters. Our methodology presents several novelties. Firstly, it can account for the encoding uncertainty by providing a wide range of encoding options: the maximum a posteriori, the marginal posterior distribution, and the effective number of letters at each given position. Secondly, our new algorithm deals with the missing data in th

SUBMITTER: Allam I 

PROVIDER: S-EPMC6033379 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature