Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens
Models of double knotted proteins predicted by AlphaFold (AlphaFold-local folder) [1] and RoseTTaFold (Rosetta folder) [2]. AlphaFold-local folder only consists of the structures predicted by locally installed version of AlphaFold (2.1.0).
TrmD-Tm1570 folder includes of the complex of TrmD-Tm1570 with four SAMs obtained via molecular docking.
[1] Jumper, John, et al. "Highly accurate protein structure prediction with AlphaFold." Nature 596.7873 (2021): 583-589.
[2] Baek, Minkyung, et al. "Accurate prediction of protein structures and interactions using a three-track neural network." Science 373.6557 (2021): 871-876.