title: O(NlogN) continuous electrostatics method for fast calculation of solvation energies of biomolecules.
abstract: We report the development of a new, fast, surface-based method for numerical calculations of the solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size, both in time and memory requirements, produces explicit values for the reaction field potential and stable values of the polar energy within only a few percent error margin practically for any molecular configurations. The method works well both for large and small molecules and thus gives stable energy differences for quantities such as the polar energy contributions to molecular complex formation energies.
authors.affiliation: Quantum Pharmaceuticals, Moscow, Russia. peter.fedichev@q-pharm.com
authors.forename: P O
authors.initials: PO
authors.lastname: Fedichev
authors.forename: E G
authors.initials: EG
authors.lastname: Getmantsev
authors.forename: L I
authors.initials: LI
authors.lastname: Menshikov
mesh_terms: D008024:Ligands; D056004:Molecular Dynamics Simulation; D011506:Proteins / Q000737:chemistry*; D012995:Solubility; D055672:Static Electricity; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D008024:Ligands; D011506:Proteins