ArticleBioinformatics (Oxford, England)2020
PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Modernizing biomolecular NMR: The POKY suite.The Journal of biological chemistry · 2026Review
- Pathological mutations in the phospholamban cytoplasmic region affect its topology and dynamics modulating the extent of SERCA inhibition.Biochimica et biophysica acta. Biomembranes · 2024Article
- ssPINE: Probabilistic Algorithm for Automated Chemical Shift Assignment of Solid-State NMR Data from Complex Protein Systems.Membranes · 2022Article
- A kink in DWORF helical structure controls the activation of the sarcoplasmic reticulum CaStructure (London, England : 1993) · 2022Article
- POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data.Journal of structural biology: X · 2022Article
- Structural basis for sarcolipin's regulation of muscle thermogenesis by the sarcoplasmic reticulum CaScience advances · 2021Article
- Structural basis for allosteric control of the SERCA-Phospholamban membrane complex by CaeLife · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationTwo-dimensional [15N-1H] separated local field solid-state nuclear magnetic resonance (NMR) experiments of membrane proteins aligned in lipid bilayers provide tilt and rotation angles for α-helical segments using Polar Index Slant Angle (PISA)-wheel models. No integrated software has been made available for data analysis and visualization.
resultsWe have developed the PISA-SPARKY plugin to seamlessly integrate PISA-wheel modeling into the NMRFAM-SPARKY platform. The plugin performs basic simulations, exhaustive fitting against experimental spectra, error analysis and dipolar and chemical shift wave plotting. The plugin also supports PyMOL integration and handling of parameters that describe variable alignment and dynamic scaling encountered with magnetically aligned media, ensuring optimal fitting and generation of restraints for structure calculation. AVAILABILITY AND IMPLEMENTATION: PISA-SPARKY is freely 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 of the SBGrid (https://sbgrid.org). The pisa.py script is available and documented on GitHub (https://github.com/weberdak/pisa.py) along with a tutorial video and sample data. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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