Publications — POKY Suite Manual

📣 Citing POKY If you use POKY in your research, please cite the POKY software paper below. The other entries describe the predecessor tools (NMRFAM-SPARKY, PINE-SPARKY, PONDEROSA) that POKY's automated assignment and structure-calculation features build on.

2026

Modernizing biomolecular NMR: The POKY suite

Chiu A, Lee W.

Journal of Biological Chemistry, 302(3):111246

DOI
2025

A-SIMA/A-MAP: a comprehensive toolkit for NMR-based metabolomics analysis

Chiu A, Rahimi M, Lee W.

Metabolomics, 21:10

DOI
2025

Automated Chemical Shift Assignments of MAS Solid-State NMR Spectra of Complex Protein Systems by ssPINE/ssPINE-POKY

Lopez Giraldo AE, Rahimi M, Lee W.

Applied Sciences, 15(12):6563

DOI
2024

REDEN: Interactive multi-fitting decomposition-based NMR peak picking assistant

Rahimi M, Chiu A, Lopez Giraldo AE, Yoon JH, Lee W.

Journal of Magnetic Resonance, 358:107600

DOI
2023

Breaking boundaries: TINTO in POKY for computer vision-based NMR walking strategies

Lopez Giraldo AE, Werner Z, Rahimi M, Lee W.

Journal of Biomolecular NMR, 77(5–6):217–228

DOI
2022

A toolset for the solid-state NMR-based 3D structure calculation of proteins

Rahimi M, Lee Y, Nguyen H, Chiu A, Lee W.

Journal of Magnetic Resonance, 339:107214

DOI
2022

ssPINE: probabilistic algorithm for automated chemical shift assignment of solid-state NMR data from complex protein systems

Dwarasala A, Rahimi M, Markley JL, Lee W.

Membranes, 12(9):834

DOI
2022

POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data

Manthey I, Tonelli M, Clos L 2nd, Rahimi M, Markley JL, Lee W.

Journal of Structural Biology: X, 6:100073

DOI
2021

POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules

Lee W, Rahimi M, Lee Y, Chiu A.

Bioinformatics, 37(18):3041–3042

DOI
2020

PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins

Weber DK, Wang S, Markley JL, Veglia G, Lee W.

Bioinformatics, 36(9):2915–2916

DOI
2018

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

Lee W, Markley JL.

Bioinformatics, 34(9):1586–1588

DOI
2016

Integrative NMR for biomolecular research

Lee W, Cornilescu G, Dashti H, Eghbalnia HR, Tonelli M, Westler WM, Butcher SE, Henzler-Wildman KA, Markley JL.

Journal of Biomolecular NMR, 64(4):307–332

DOI
2015

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

Lee W, Tonelli M, Markley JL.

Bioinformatics, 31(8):1325–1327

PubMed
2014

PONDEROSA-C/S: client-server based software package for automated protein 3D structure determination

Lee W, Stark JL, Markley JL.

Journal of Biomolecular NMR, 60(2–3):73–75

PubMed
2011

PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination

Lee W, Kim JH, Westler WM, Markley JL.

Bioinformatics, 27(12):1727–1728

PubMed
2009

PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy

Lee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JL.

Bioinformatics, 25(16):2085–2087

PubMed

🔎 Complete & up-to-date list

For the complete, current list of Lee Research Group publications (including methods built on top of POKY), see Google Scholar or the official POKY Team website.