Allostery is a constitutive, albeit often elusive, feature of biomolecular systems, which heavily determines their functioning. Its mechanical, entropic, long-range, ligand, and environment-dependent nature creates far from trivial interplays between residues and, in general, the secondary structure of proteins. This intricate scenario is mirrored in computational terms as different notions of “correlation” among residues and pockets can lead to different conclusions and outcomes. In this article, we put on a common ground and challenge three computational approaches for the correlation estimation task and apply them to three diverse targets of pharmaceutical interest: the androgen A2A receptor, the androgen receptor, and the EGFR kinase domain. Results show that partial results consensus can be attained, yet different notions lead to pointing the attention to different pockets and communications.
On the allosteric puzzle and pocket crosstalk through computational means
Note: This paper is part of the JCP Special Topic on New Views of Allostery.
Riccardo Aguti, Mattia Bernetti, Stefano Bosio, Sergio Decherchi, Andrea Cavalli; On the allosteric puzzle and pocket crosstalk through computational means. J. Chem. Phys. 28 April 2023; 158 (16): 165101. https://doi.org/10.1063/5.0145364
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