Automated protein motif generation in the structure-based protein function prediction tool ProMOL.

ABSTRACT: ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entr

SUBMITTER: Osipovitch M 

PROVIDER: S-EPMC4684744 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature