PINE-SPARKY.2 for automated NMR-based protein structure research.

ABSTRACT

Summary: Nuclear magnetic resonance (NMR) spectroscopy, along with X-ray crystallography and cryoelectron microscopy, is one of the three major tools that enable the determination of atomic-level structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR studies, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models. Availability and implementation PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison (http//pine.nmrfam.wisc.edu/download_packages.html), the NMRbox Project (https//nmrbox.org) and to subscribers to the SBGrid (https//sbgrid.org). For a detailed description of the program, see http//www.nmrfam.wisc.edu/pine-sparky2.htm. Contact whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu. Supplementary information Supplementary data are available at Bioinformatics online.