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SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses

A. Pecina, S. Haldar, J. Fanfrlík, R. Meier, J. Řezáč, M. Lepšík, P. Hobza,

. 2017 ; 57 (2) : 127-132. [pub] 20170117

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/bmc17031171

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 Zn(2+)···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.

Citace poskytuje Crossref.org

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$a Fanfrlík, Jindřich $u Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
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$a Meier, René $u Leibniz Institute of Plant Biochemistry , Weinberg 3, 06120 Halle, Germany.
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$a Řezáč, Jan $u Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
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$a Lepšík, Martin $u Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic , v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
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$a Hobza, Pavel $u 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.
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