dorsal/arxiv
View SchemaThe minimal molecular surface
| Authors | P. W. Bates, G. W. Wei, Shan Zhao |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0610038 |
| URL | https://arxiv.org/abs/q-bio/0610038 |
Abstract
We introduce a novel concept, the minimal molecular surface (MMS), as a new paradigm for the theoretical modeling of biomolecule-solvent interfaces. When a less polar macromolecule is immersed in a polar environment, the surface free energy minimization occurs naturally to stabilizes the system, and leads to an MMS separating the macromolecule from the solvent. For a given set of atomic constraints (as obstacles), the MMS is defined as one whose mean curvature vanishes away from the obstacles. An iterative procedure is proposed to compute the MMS. Extensive examples are given to validate the proposed algorithm and illustrate the new concept. We show that the MMS provides an indication to DNA-binding specificity. The proposed algorithm represents a major step forward in minimal surface generation.
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"abstract": "We introduce a novel concept, the minimal molecular surface (MMS), as a new\nparadigm for the theoretical modeling of biomolecule-solvent interfaces. When a\nless polar macromolecule is immersed in a polar environment, the surface free\nenergy minimization occurs naturally to stabilizes the system, and leads to an\nMMS separating the macromolecule from the solvent. For a given set of atomic\nconstraints (as obstacles), the MMS is defined as one whose mean curvature\nvanishes away from the obstacles. An iterative procedure is proposed to compute\nthe MMS. Extensive examples are given to validate the proposed algorithm and\nillustrate the new concept. We show that the MMS provides an indication to\nDNA-binding specificity. The proposed algorithm represents a major step forward\nin minimal surface generation.",
"arxiv_id": "q-bio/0610038",
"authors": [
"P. W. Bates",
"G. W. Wei",
"Shan Zhao"
],
"categories": [
"q-bio.BM",
"q-bio.QM"
],
"title": "The minimal molecular surface",
"url": "https://arxiv.org/abs/q-bio/0610038"
},
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"type": "Model",
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