title: DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes.
abstract: We introduce the new knowledge-based scoring function DSX that consists of distance-dependent pair potentials, novel torsion angle potentials, and newly defined solvent accessible surface-dependent potentials. DSX pair potentials are based on the statistical formalism of DrugScore, extended by a much more specialized set of atom types. The original DrugScore-like reference state is rather unstable with respect to modifications in the used atom types. Therefore, an important method to overcome this problem and to allow for robust results when deriving pair potentials for arbitrary sets of atom types is presented. A validation based on a carefully prepared test set is shown, enabling direct comparison to the majority of other popular scoring functions. Here, DSX features superior performance with respect to docking- and ranking power and runtime requirements. Furthermore, the beneficial combination with torsion angle-dependent and desolvation-dependent potentials is demonstrated. DSX is robust, flexible, and capable of working together with special features of popular docking engines, e.g., flexible protein residues in AutoDock or GOLD. The program is freely available to the scientific community and can be downloaded from our Web site  www.agklebe.de .
authors.affiliation: Department of Pharmaceutical Chemistry, Philipps-Universität Marburg, Marbacher Weg 6, Germany.
authors.forename: Gerd
authors.initials: G
authors.lastname: Neudert
authors.forename: Gerhard
authors.initials: G
authors.lastname: Klebe
mesh_terms: D019295:Computational Biology / Q000379:methods*; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism*; D011789:Quantum Theory; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D008024:Ligands; D011506:Proteins