DEEPSAM: A Hybrid Evolutionary Algorithm for the Prediction of Biomolecules Structure

Goldstein, Moshe

doi:10.1007/978-3-319-39636-1_16

Cited by 3 publications

(2 citation statements)

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“…Also, we expect that at the experimental temperatures the minimum of the free energy potential surface will effectively be the lowest-energy structure on the potential energy surface (PES). Thus, here, like in a previous study, DEEPSAM, , a PES global minimization algorithm developed in our group, which is built upon the extensively used TINKER , molecular modeling software package, was employed to search for the global minimum of the PES of charge states of UBQ 6+. DEEPSAM was run to predict UBQ 6+ conformations, each one for a different charge distribution.…”

Section: Application Systems and Methodsmentioning

confidence: 99%

“…The paper is divided into the following sections: in the Application Systems and Methods section, our structure prediction algorithm, called DEEPSAM ( D iffusion E quation E volutionary P rogramming S imulated A nnealing M ethod) , along with CCS calculations is briefly described and alternative UBQ 6+ charge distributions studied here are presented in detail; in the Results and Discussion section, the predicted structures for those alternative UBQ 6+ charge distributions are presented and analyzed, including comparisons with experimental data; in the Concluding Remarks section, our conclusions are presented together with a preview of possible further developments.…”

Section: Introductionmentioning

confidence: 99%

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Conformers of Ubiquitin 6+ for Different Charge Distributions: Atomistic Structures and Ion Mobility Cross Sections

et al. 2019

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Despite the fact that protein chemistry occurs in solution, studying the structure of desolvated proteins in mass spectrometry vacuum conditions allows one to study biological molecules in complete isolation. The electrospray ionization process results in charged protein conformers for which the charge locations distribution and the corresponding structure are not known. In this paper, we explore the influence of different charge distributions on the structure of conformers of ubiquitin 6+ in the vacuum conditions of mass spectrometry. Using the Tinker implementation of the AMBER99FF force field, the atomistic lowest-energy structures for those charge distributions were calculated by the DEEPSAM algorithm. Differences among the calculated structures are analyzed and discussed in terms of the relation to experimentally observable ion mobility mass spectrometry cross sections. They also are compared to the neutral ubiquitin's native structure and to the nearly linear structure of the ubiquitin 13+ ion. In general, different charge distributions lead to substantially different structures and ion mobility cross sections. In this study, however, it was found that this is not always the case. Our conclusion is that measurements of ion mobility cross sections cannot be used to help determine a unique charge distribution because different charge distributions lead to structures that approximately agree in terms of experimental cross sections.

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