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Bioinformatics. 2018 May 1;34(9):1586-1588. doi: 10.1093/bioinformatics/btx785.

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

Author information

1
National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA.

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.

PMID:
29281006
PMCID:
PMC5925765
DOI:
10.1093/bioinformatics/btx785
[Indexed for MEDLINE]
Free PMC Article

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