{"data":{"id":59,"name":"High-Throughput Coarse-Grained Simulations for Permeability Prediction","abbreviation":"MDCG","description":"<p>This method employs high-throughput coarse-grained (HTCG) molecular dynamics simulations to derive a permeability surface across chemical space. Instead of evaluating compounds one by one at the atomistic level, small organic molecules are represented using Martini coarse-graining, which drastically reduces computational cost while preserving accurate thermodynamics. The permeability surface is expressed in terms of two experimentally accessible molecular descriptors: bulk partitioning free energy and pKa. By systematically simulating coarse-grained analogs of hundreds of thousands of compounds, the approach identifies how hydrophobicity and ionization state govern passive permeation across lipid bilayers. The resulting surface allows prediction of permeability coefficients with accuracy comparable to atomistic simulations, while enabling inverse design strategies that link chemical functional groups to permeability. This HTCG framework provides a physics-based, scalable alternative to QSPR and experimental screening.<\/p>","categories":[{"id":13,"title":"Coarse grain MD","breadcrumb":[{"id":6,"title":"Simulated"},{"id":13,"title":"Coarse grain MD"}]}],"url":"https:\/\/molmedb.upol.cz\/api\/v1\/methods\/59","landing_page":"https:\/\/molmedb.upol.cz\/method\/59","created_at":"2020-01-27T14:15:27.000000Z","updated_at":"2026-07-09T06:33:01.000000Z"}}