Summary
Structure prediction neural networks predict different conformations of a given sequence depending on if a single chain is predicted vs. multiple chains (1,2).
1.
Jendrusch MA, Yang ALJ, Cacace E, Bobonis J, Voogdt CGP, Kaspar S, et al. AlphaDesign: a de novo protein design framework based on AlphaFold. Molecular Systems Biology. 2025;21(9):1166–89. Available from: https://doi.org/10.1038/s44320-025-00119-z
2.
Cummins MC, Jacobs TM, Teets FD, DiMaio F, Tripathy A, Kuhlman B. AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein. Protein Science. 2022;31(7). Available from: https://doi.org/10.1002/pro.4368