What is POKY?POKY is a comprehensive, AI-integrated software suite for multidimensional NMR data analysis, automated resonance assignment, 3D structure calculation, and computer-aided drug design and metabolomics — developed by Prof. Woonghee Lee and the POKY Team at the University of Colorado Denver.
POKY goes far beyond a traditional spectrum viewer: it combines the familiar interactive spectral analysis workflow with deep-learning structure prediction (AlphaFold 2/3, ESMFold, Boltz-2, Chai-1), automated backbone/sidechain assignment (I-PINE, PINE-SPARKY.2, APES, iPick), solid-state NMR analysis (ssPINE, PISA-SPARKY), small-molecule and metabolomics identification (A-SIMA, A-MAP, DeepSAT), virtual screening (POKY DOCK), and scriptable automation through POKY Notepad and POKY Notebooks — all in one unified interface. See the up-to-date feature list on the official POKY website.
Supported Platforms
| Platform | Requirements | Executable |
|---|---|---|
| 🍎 macOS | XQuartz 2.8.6+; Rosetta 2 (Apple Silicon) | poky.app |
| 🪟 Windows | Microsoft Visual C++ Redistributable | C:\poky_win\bin\poky.bat |
| 🐧 Linux | Ubuntu 20.04+ / RHEL-compatible; libxcb | poky_linux/bin/poky.sh |
| 📦 HPC/Container | Singularity / Apptainer | apptainer run --writable poky.sif |
👉 See the Installation Guide for step-by-step instructions for each platform.
Key Features
Main Window & POKY Automation Guide (PAG)
The POKY main window provides three tabbed sections: Experiments, Resonances, and the POKY Automation Guide (PAG). PAG organizes all automation tools and workflows for your study type — protein NMR (solution), MAS solid-state, metabolomics, or oriented solid-state.
- Drag-and-drop spectra from Finder/Explorer/Nautilus directly into the Experiments tab
- Non-.ucsf formats (Bruker 2rr/3rrr/4rrrr, NMRPipe .ft2/.ft3/.ft4, NMRView .nv, Varian, JCAMP-DX .jdx/.dx) auto-converted
- Five-level Tree List: Molecule → Condition → Dimension → Spectrum → View
- Shift/peak list import/export with a single click
Structure Calculation & Prediction
- POKY Structure Builder (Pb) — one-click 3D structure calculation setup from your active project (PONDEROSA)
- POKY Structure Analyzer (Pa) — validate PONDEROSA outputs interactively with PyMOL
- PONDEROSA-C/S web server — automated NOE assignment (AUDANA/AUDASA) and XPLOR-NIH structure calculation on POKY's servers, submitted with c3 or Pb
- Deep-learning structure prediction built in: AlphaFold 2/3, ESMFold, BOLTZ-2, CHAI-1, and D-I-TASSER
- CS-Rosetta, TALOS-N, TAPAS, and PONDEROSA-based NMR-restrained structure prediction
Automated & AI-Assisted Assignment
- AI-assisted peak picking (APES, iPick) and automated solution protein NMR assignment (I-PINE/PINE-SPARKY.2, MAGIC, ARSIGN)
- Versatile Assigner and Predict-and-Confirm superfast sidechain assignment referencing PACSY
- Chemical shift validation with pyLACS and secondary structure prediction with pyPECAN
- Solid-state NMR support: ssPINE automated assignment and PISA-SPARKY PISA wheel analysis
Beyond Protein NMR
- Nucleic acid analysis: automated imino assignment (RNA-PAIRS), RNA secondary structure prediction (MXfold2)
- Small molecule & metabolomics identification: A-SIMA, A-MAP, DeepSAT, COLMAR-HSQC
- In silico screening: POKY DOCK virtual screening and binding-site prediction (IF-SitePred)
- Chemical shift perturbation, titration, and relaxation (T₁/T₂/hetNOE) analysis
Scripting & Automation
- Full Python environment with NumPy, SciPy, Matplotlib, scikit-learn, and more
- POKY Notepad (Pn) — advanced script editor for batch tasks, with a library of ready-made scripts
- POKY Notebooks (PN) — Jupyter notebook workflows hosted alongside POKY
- Command Finder (cf) — search every two-letter command, Notepad script, and Notebook from one dialog — see Command Reference
Manual Topics
- Introduction to POKY — basic concepts, starting POKY, opening spectra
- Installation — download & platform-specific setup
- Spectrum Views — contour levels, overlays, zooming, printing
- Peaks & Assignments — picking, assigning, integrating, listing
- Python Extensions — writing and running POKY extensions
- Automatic Assignment — I-PINE, PINE-SPARKY.2, Versatile Assigner
- PRIDE (Relaxation & Dynamics) — T1/T2/R1/R2, TauC/M.W., HetNOE, SEA-TROSY, TRACT, Model-Free, RCI/S²
- Proky (Processing) — Quick Convert, Process 1D/nD, Batch Processing, NMRPipe + Phaser, Pseudo-2D T1/T2
- CAFE (CSP & Kd) — Chemical Shift Perturbation mapping and Kd binding-affinity fitting
- P-Mix (Mixture Design) — simulated-annealing compound mixture design for 1D NMR screening
- LigLib (Lignin NMR Library) — browse/search lignin & cell wall model compound NMR shifts and match them to peaks
- MetaLib (Shared Library Cache) — the download-on-demand reference-library convention behind A-SIMA, P-Mix, and LigLib
- Command Reference — all POKY two-letter commands
- AI Chat Assistant — chat with Claude, ChatGPT, or Gemini via their API, with live POKY session context included
- PACSYLLM Database Search — ask POKY LLM natural-language questions about real chemical shift and structure statistics from the PACSYLLM database
- PONDEROSA-C/S (Structure Calculation) — submitting structure calculations from POKY (c3, Pb), inputs, the results page and downloads
- TAPAS (Torsion & SS Prediction) — φ/ψ/ω/χ1/χ2, secondary structure, RCI-S2 and SASA from chemical shifts with per-residue reliability (Ts)
- Job Dashboards (Web Servers) — the results web pages of PONDEROSA-C/S, MolProbity, TALOS-N/TALOS+, TAPAS, I-PINE and I-ssPINE jobs, and how to use them
- File Formats — .ucsf, .proj, .save, NMR-STAR (.str), NEF (.nef), and more
- Miscellaneous — keyboard shortcuts, pointer modes, preferences
- Video Tutorials — embedded YouTube tutorials by topic
- Publications — Lee Group journal articles
📺 Featured Tutorial
Get started with POKY in under 10 minutes. More tutorials are available on the Video Tutorials page or on the YouTube channel.
🔗 Quick Links
📖 Citing POKY
If you use POKY in your research, please cite:
Lee W, Rahimi M, Lee Y, Chiu A. (2021). POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. Bioinformatics, 37(18):3041–3042. [DOI]
See the Publications page for the complete list of related papers.