Using support vector machines to improve elemental ion identification in macromolecular crystal structures.

ABSTRACT: In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were cons

SUBMITTER: Morshed N 

PROVIDER: S-EPMC4427199 | biostudies-literature | 2015 May

REPOSITORIES: biostudies-literature