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Classical force fields (FFs) remain the workhorse for large-scale simulations even as machine-learned interatomic potentials (MLIPs) approach ab initio accuracy. They decompose total configuration energies into simple effective interactions whose parameters are traditionally assigned based on atom or bond types, enabli...
Membrane targeting regulates protein localization and function. Abl and Src kinase feature an N-terminal myristoylation site followed by an intrinsically disordered region (IDR) of positive net charge, suggesting these regions contribute to membrane targeting. We investigated the interplay of myristoylation and IDR bin...
This work proposes BackFlip-2: a fast SE(3)-equivariant graph neural network trained to directly predict dynamical descriptors, such as directional backbone flexibility and pairwise dynamic correlations, from an equilibrium structure, and shows that the proposed equivariant architecture is especially well-suited for ca...
A comprehensive benchmark of Martini 3 variations intended for IDPs up to 809 amino acids in length is presented and the behavior of four well-known Martini 3 variations for IDPs are compared.
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