Natural products with different structural scaffolds and relatively large molecular weights (up to 2,000 Da) provide a rich pool of drug candidates and play an important role in discovery of new therapeutics with analgesic, anti-infective, anticancer, antibacterial, antiviral, antiparasitic, and other activity for treatment of human diseases. However, conversion of natural products to effective therapeutics is often restricted by their poor cell-permeability, which prevents intestinal absorption and crossing of the blood-brain-barrier.

PerMM is a web-based tool for analysis of different aspects of interaction of molecules with biological membranes, including their binding affinities to membranes, energy barriers along the membrane normal, and permeability coefficients. This tool implements novel computational method based on physically realistic description of interactions of molecules with the lipid bilayer aimed to quantitatively describe their translocation across the lipid bilayer.

PerMM can be applied for study of interactions of diverse compounds ranging from small organic molecules to cyclic peptides and peptidomimetcs with different artificial and natural membranes (including blood-brain-barrier and gut epithelium). The server was developed to assist investigators at early stages of drug development in optimization of cell permeability of new therapeutics derived from natural products.

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