CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery

Hongzhao Shao; Stephen Boulton; Cristina Olivieri; Hebatallah Mohamed; Madoka Akimoto; Manu Veliparambil Subrahmanian; Gianluigi Veglia; John L Markley; Giuseppe Melacini; Woonghee Lee

doi:10.1093/bioinformatics/btaa781

CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery

Bioinformatics. 2021 May 23;37(8):1176-1177. doi: 10.1093/bioinformatics/btaa781.

Authors

Affiliations

¹ Department of Chemistry and Chemical Biology, Hamilton, ON L8S 4L8, Canada.
² Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
³ Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, MN 55455, USA.
⁴ Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.
⁵ Biochemistry Department, National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53717, USA.
⁶ Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA.

Abstract

Motivation: Correlated Nuclear Magnetic Resonance (NMR) chemical shift changes identified through the CHEmical Shift Projection Analysis (CHESPA) and CHEmical Shift Covariance Analysis (CHESCA) reveal pathways of allosteric transitions in biological macromolecules. To address the need for an automated platform that implements CHESPA and CHESCA and integrates them with other NMR analysis software packages, we introduce here integrated plugins for NMRFAM-SPARKY that implement the seamless detection and visualization of allosteric networks.

Availability and implementation: CHESCA-SPARKY and CHESPA-SPARKY are 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). The assigned spectra involved in this study and tutorial videos using this dataset are available at https://sites.google.com/view/chescachespa-sparky.

Supplementary information: Supplementary data are available at Bioinformatics Online.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Data Analysis*
Magnetic Resonance Spectroscopy
Nuclear Magnetic Resonance, Biomolecular
Proteins
Software*

Substances

Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding