تقرير
EXCOGITO, an extensible coarse-graining toolbox for the investigation of biomolecules by means of low-resolution representation
| العنوان: | EXCOGITO, an extensible coarse-graining toolbox for the investigation of biomolecules by means of low-resolution representation |
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| المؤلفون: | Giulini, Marco, Fiorentini, Raffaele, Tubiana, Luca, Potestio, Raffaello, Menichetti, Roberto |
| سنة النشر: | 2024 |
| المجموعة: | Condensed Matter Physics (Other) |
| مصطلحات موضوعية: | Condensed Matter - Soft Condensed Matter, Condensed Matter - Statistical Mechanics, Physics - Biological Physics |
| الوصف: | Bottom-up coarse-grained (CG) models proved to be essential to complement and sometimes even replace all-atom representations of soft matter systems and biological macromolecules. The development of low-resolution models takes the moves from the reduction of the degrees of freedom employed, that is, the definition of a mapping between a system's high-resolution description and its simplified counterpart. Even in the absence of an explicit parametrisation and simulation of a CG model, the observation of the atomistic system in simpler terms can be informative: this idea is leveraged by the mapping entropy, a measure of the information loss inherent to the process of coarsening. Mapping entropy lies at the heart of the extensible coarse-graining toolbox, or EXCOGITO, developed to perform a number of operations and analyses on molecular systems pivoting around the properties of mappings. EXCOGITO can process an all-atom trajectory to compute the mapping entropy, identify the mapping that minimizes it, and establish quantitative relations between a low-resolution representation and the geometrical, structural, and energetic features of the system. Here, the software, which is available free of charge under an open-source licence, is presented and showcased to introduce potential users to its capabilities and usage. Published on the J. Chem. Inf. Model. on June 11, 2024. DOI: https://doi.org/10.1021/acs.jcim.4c00490 |
| نوع الوثيقة: | Working Paper |
| URL الوصول: | http://arxiv.org/abs/2403.08097 |
| رقم الأكسشن: | edsarx.2403.08097 |
| قاعدة البيانات: | arXiv |
| الوصف غير متاح. |