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

Bartels C, Guntert P, Billeter M, Wuthrich K (1997) GARANT-a general algorithm for resonance assignment of multidimensional nuclear magnetic resonance spectra. J Comput Chem 18:139–149

Article  Google Scholar 

Bishop AC, Torres-Montalvo G, Kotaru S, Mimun K, Wand AJ (2023) Robust automated backbone triple resonance NMR assignments of proteins using Bayesian-based simulated annealing. Nat Commun 14:1556

Article  ADS  Google Scholar 

Cheng Y, Gao X, Liang F (2014) Bayesian peak picking for NMR spectra. Genom Proteom Bioinform 12:39–47

Article  Google Scholar 

Dutta SK et al (2015) APSY-NMR for protein backbone assignment in high-throughput structural biology. J Biomol NMR 61:47–53

Article  Google Scholar 

Dwarasala A, Rahimi M, Markley JL, Lee W (2022) ssPINE: probabilistic algorithm for automated chemical shift assignment of solid-state NMR data from complex protein systems. Membranes 12:834

Article  Google Scholar 

Garrett, D. S., Gronenborn, A. M. & Marius Clore, G. (2011) A short recollection on the paper entitled “A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams” by D.S. Garrett, R. Powers, A.M. Gronenborn, and G.M. Clore [J. Magn. Reson. 95 (1991) 214–220]. J Magn Reson 213:364–365

Jolliffe IT, Cadima J (2016) Principal component analysis: a review and recent developments. Phil Trans R Soc A 374:20150202

Article  ADS  MathSciNet  MATH  Google Scholar 

Koradi R, Billeter M, Engeli M, Güntert P, Wüthrich K (1998) Automated peak picking and peak integration in macromolecular NMR spectra using AUTOPSY. J Magn Reson 135:288–297

Article  ADS  Google Scholar 

Lee W, Tonelli M, Markley JL (2015) NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinformatics 31:1325–1327

Article  Google Scholar 

Lee W et al (2019) I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR 73:213–222

Article  Google Scholar 

Lee W, Rahimi M, Lee Y, Chiu A (2021) POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. Bioinformatics 37:3041–3042

Article  Google Scholar 

Lee Y et al (2021) pH-dependent polymorphism of the structure of SARS-CoV-2 nsp7. bioRxiv. https://doi.org/10.1101/2021.09.10.459800

Article  Google Scholar 

López-Giraldo AE et al (2020) The three-dimensional structure of the toxic peptide Cl13 from the scorpion centruroides limpidus. Toxicon 184:158–166

Article  Google Scholar 

Manthey I et al (2022) POKY software tools encapsulating assignment strategies for solution and solid-state protein NMR data. J Struct Biol: X 6:100073

Google Scholar 

Nawrocka EK, Dahan D, Kazimierczuk K, Olbratowski P (2022) Radon peak-picker based on a neural network. J Magn Reson Open 12–13:100083

Rahimi M, Lee Y, Markley JL, Lee W (2021) iPick: Multiprocessing software for integrated NMR signal detection and validation. J Magn Reson 328:106995

Shin J, Lee W, Lee W (2008) Structural proteomics by NMR spectroscopy. Expert Rev Proteomics 5:589–601

Article  Google Scholar 

Wang Z, Bovik AC, Sheikh HR, Simoncelli EP (2004) Image quality assessment: from error visibility to structural similarity. IEEE Trans on Image Process 13:600–612

Article  ADS  Google Scholar 

Xu J, Van Doren SR (2018) Affinities and comparisons of enzyme states by principal component analysis of NMR spectra, automated using TREND software. Methods Enzymol 607:217–240

Article  Google Scholar 

Zimmerman DE et al (1997) Automated analysis of protein NMR assignments using methods from artificial intelligence. J Mol Biol 269:592–610

Article  Google Scholar 

留言 (0)

沒有登入
gif