References
[1] Vakser, I. A., Protein-protein docking: From interaction to
interactome. Biophys. J. 2014, 107 , 1785-1793.
[2] Moal, I. H., Moretti, R., Baker, D., Fernandez-Recio, J.,
Scoring functions for protein–protein interactions. Curr. Opin.
Struct. Biol. 2013, 23 , 862–867.
[3] Jumper, J., Evans, R., Pritzel, A., Green, T., et al. ,
Highly accurate protein structure prediction with AlphaFold.Nature 2021, 596 , 583-589.
[4] Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.
A., et al. , Molecular surface recognition: Determination of
geometric fit between proteins and their ligands by correlation
techniques. Proc. Natl. Acad. Sci. USA 1992, 89 ,
2195-2199.
[5] Kundrotas, P. J., Zhu, Z., Janin, J., Vakser, I. A., Templates
are available to model nearly all complexes of structurally
characterized proteins. Proc. Natl. Acad. Sci. USA 2012,109 , 9438–9441.
[6] Evans, R., O’Neill, M., Pritzel, A., Antropova, N., et
al. , Protein complex prediction with AlphaFold-Multimer. bioRxiv2022, doi:org/10.1101/2021.10.04.463034 .
[7] Baek, M., DiMaio, F., Anishchenko, I., Dauparas, J., et
al. , Accurate prediction of protein structures and interactions using a
three-track neural network. Science 2021, 373 , 871-876.
[8] Wodak, S. J., Vajda, S., Lensink, M. F., Kozakov, D., Bates, P.
A., Critical assessment of methods for predicting the 3D structure of
proteins and protein complexes. Ann. Rev. Bioph. 2023, 52 ,
183-206.
[9] Heo, L., Sugita, Y., Feig, M., Protein assembly and crowding
simulations. Curr. Opin. Struct. Biol. 2022, 73 , 102340.
[10] Vakser, I. A., Deeds, E. J., Computational approaches to
macromolecular interactions in the cell. Curr. Opin. Struct.
Biol. 2019, 55 , 59-65.
[11] Vakser, I. A., Grudinin, S., Jenkins, N. W., Kundrotas, P. J.,
Deeds, E. J., Docking-based long timescale simulation of cell-size
protein systems at atomic resolution. Proc. Natl. Acad. Sci. USA2022, 119 , e2210249119.
[12] Schweke, H., Xu, Q., Tauriello, G., Pantolini, L., et
al. , Discriminating physiological from non-physiological interfaces in
structures of protein complexes: A community-wide study.Proteomics 2023.