2006/10/20 by Peter W. Bates, Gang Wei, Bates, P. W. +3
Biochemistry, Genetics and Molecular Biology · Engineering · #Advanced biosensing and bioanalysis techniques #Biomolecules (q-bio.BM) #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #Molecular Junctions and Nanostructures #Quantitative Methods (q-bio.QM)
paper · pdf · doi:10.48550/arxiv.q-bio/0610038
openalex publication_date 2006/10/20 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.