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The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates.

Recently, the Little Dragon Two and Poly-Dragon multivariate based public-key cryptosystems were proposed as efficient and secure schemes. In particular, the inventors of the two schemes claim that Little Dragon Two and Poly-Dragon resist algebraic cryptanalysis. In this paper, we show that MXL2, an algebraic attack method based on the XL algorithm and Ding’s concept of Mutants, is able to break Little Dragon Two with keys of length up to 229 bits and Poly-Dragon with keys of length up to 299. This contradicts the security claim for the proposed schemes and demonstrates the strength of MXL2 and the Mutant concept. This strength is further supported by experiments that show that in attacks on both schemes the MXL2 algorithm outperforms the Magma’s implementation of F4.

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