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SUMMARY:Integrated software technologies for biomolecular NMR studies
LOCATION:Chemistry A101
TZID:America/Denver
DTSTART:20221027T160000
UID:2026-04-28-13-31-53@natsci.colostate.edu
DTSTAMP:20260428T133153
Description:About the Seminar\n\nWe develop the POKY suite which is the rev
 olutionized platform with boundless possibilities for advancing research a
 nd technology development in biomolecular studies. The “POKY” is the c
 ore of the Integrative NMR platform providing a fully integrated professio
 nal-grade cyberinfrastructure. The next level automation and visualization
  maximizing the quality of user experience and productivity will be enable
 d by the `full-stack development’ of artificial intelligence (AI)\, mach
 ine learning (ML)\, computer vision (CV)\, and other modern technologies. 
 As well as routine automated studies on well-behaving proteins\, it also k
 eeps up with the recent advances in the field such as 13C-detected solutio
 n NMR for intrinsically disordered proteins (IDPs) and 1H/13C/19F detected
  solid-state NMR for large\, insoluble and membrane proteins. Different le
 vel users will be able to use different interface tools such as step-by-st
 ep guided automations (POKY Automation Guide)\, high-level push buttons (P
 OKY Extensions)\, intermediate-level Jupyter notebooks (POKY Notebooks)\, 
 and low-level customizable scripts (POKY Notepad). In this presentation\, 
 I will show how POKY makes NMR-based structural studies more accessible an
 d automated with practical examples.\n\nReferences\n\n 	Lee W\, Rahimi M\,
  Lee Y\, Chiu A. POKY: a software suite for multidimensional NMR and 3D st
 ructure calculation of biomolecules. Bioinformatics. 2021 Sep. 15\; 37(18)
 :3041-3042.\n 	Rahimi M\, Lee Y\, Nguyen H\, Chiu A\, Lee W. A Toolset for
  the Solid-state NMR-based 3D Structure Calculation of Proteins. Journal o
 f Magnetic Resonance. 2022 June\; 339:107214.\n 	Manthey I\, Tonelli M\, C
 los L II\, Rahimi M\, Markley JL\, Lee W. POKY software tools encapsulatin
 g assignment strategies for solution and solid-state protein NMR data. Jou
 rnal of Structural Biology: X. 2022 Aug 28\; 6:100073.\n 	Dwarasala A\, Ra
 himi M\, Markley JL\, Lee W. ssPINE: a probabilistic algorithm for automat
 ed chemical shift assignment of solid-state NMR data. Membranes. 2022\; 12
 (9): 834.\n\n&nbsp\;\n\nAbout the Speaker\n\nDr. Woonghee Lee is an Assist
 ant Professor of Chemistry at the University of Colorado Denver (CU Denver
 ). Dr. Lee completed his Ph.D. at the University of Wisconsin-Madison from
  the Integrated Program in Biochemistry (IPiB) under the guidance of Dr. J
 ohn Markley after receiving his B.S. and M.S. in Biochemistry from Yonsei 
 University under the guidance of Dr. Weontae Lee. Before joining CU Denver
  in 2020\, Dr. Lee was a principal investigator and a staff scientist at t
 he National Magnetic Resonance Facility At Madison (NMRFAM) after a short 
 postdoctoral training at NMRFAM. Additionally\, Dr. Lee was a professional
  computer programmer for three years at EnGIS technologies developing geog
 raphic information system (GIS) programs. Dr. Lee’s unique interdiscipli
 nary background has enabled him to make indispensable components of the NM
 R research platform considered field standards such as I-PINE and NMRFAM-S
 PARKY\, which are succeeded by the POKY suite. 4:00 pm
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