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

By Woonghee Lee, John L. Markley. 2017

28 citations recorded by the source corpus.

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. Supplementary information Supplementary data are available at Bioinformatics online.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Woonghee Lee
2. John L. Markley
3. Marco Tonelli
4. Mehdi Rahimi
5. Ira Manthey
6. L. Ii
7. Torsten Schwede

In Molecular Biology

1. Woonghee Lee
2. John L. Markley
3. Marco Tonelli
4. Mehdi Rahimi
5. Ira Manthey
6. L. Ii
7. Gabriel Cornilescu
8. Torsten Schwede

In Spectroscopy

1. John L. Markley
2. Woonghee Lee

Citations in the corpus

• POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data (2022, methodology): “The I-PINE webserver can be accessed using the PINE-SPARKY.2 plugin (two-letter-code ep ) in POKY .”