EXCOGITO, an extensible coarse-graining toolbox for the investigation of biomolecules by means of low-resolution representation
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arXiv
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| Format: | Preprint |
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2024
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| author | Giulini, Marco Fiorentini, Raffaele Tubiana, Luca Potestio, Raffaello Menichetti, Roberto |
| author_facet | Giulini, Marco Fiorentini, Raffaele Tubiana, Luca Potestio, Raffaello Menichetti, Roberto |
| contents | 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 |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2403_08097 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | EXCOGITO, an extensible coarse-graining toolbox for the investigation of biomolecules by means of low-resolution representation Giulini, Marco Fiorentini, Raffaele Tubiana, Luca Potestio, Raffaello Menichetti, Roberto Soft Condensed Matter Statistical Mechanics Biological Physics 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 |
| title | EXCOGITO, an extensible coarse-graining toolbox for the investigation of biomolecules by means of low-resolution representation |
| topic | Soft Condensed Matter Statistical Mechanics Biological Physics |
| url | https://arxiv.org/abs/2403.08097 |