title: SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses.
abstract: We have recently introduced the "SQM/COSMO" scoring function which combines a semiempirical quantum mechanical description of noncovalent interactions at the PM6-D3H4X level and the COSMO implicit model of solvation. This approach outperformed standard scoring functions but faced challenges with a metalloprotein featuring a Zn2+···S-interaction. Here, we invoke SCC-DFTB3-D3H4, a higher-level SQM method, and observe improved behavior for the metalloprotein and high-quality results for the other systems. This method holds promise for diverse protein-ligand complexes including metalloproteins.
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
authors.forename: Adam
authors.initials: A
authors.lastname: Pecina
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
authors.forename: Susanta
authors.initials: S
authors.lastname: Haldar
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
authors.forename: Jindřich
authors.initials: J
authors.lastname: Fanfrlík
authors.affiliation: Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle, Germany.
authors.forename: René
authors.initials: R
authors.lastname: Meier
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
authors.forename: Jan
authors.identifier: 0000-0001-6849-7314
authors.initials: J
authors.lastname: Řezáč
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Lepšík
authors.affiliation: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.|Regional Centre of Advanced Technologies and Materials, Palacký University , 77146 Olomouc, Czech Republic.
authors.forename: Pavel
authors.identifier: 0000-0001-5292-6719
authors.initials: P
authors.lastname: Hobza
mesh_terms: D008024:Ligands; D008667:Metalloproteins / Q000378:metabolism*; D011485:Protein Binding; D011789:Quantum Theory; D013816:Thermodynamics
chemical_list: D008024:Ligands; D008667:Metalloproteins