Docking of oligopeptides

• Published in: Russian chemical bulletin Vol. 68; no. 9; pp. 1780 - 1786
• Main Authors: Sulimov, A. V., Kutov, D. K., Ilin, I. S., Shikhaliev, Kh. S., Zheltkov, D. A., Tyrtyshnikov, E. E., Sulimov, V. B.
• Format: Journal Article
• Language: English
• Published: New York Springer US 01-09-2019; Springer Nature B.V
• Subjects: Algorithms; Chemistry; Chemistry and Materials Science; Chemistry/Food Science; Coordination compounds; Degrees of freedom; Docking; Full Articles; Global optimization; Inorganic Chemistry; Ligands; Organic Chemistry; Proteins; Tensors; tensor train; docking; molecular modeling; drug design
• ISSN: 1066-5285; 1573-9171
• DOI: 10.1007/s11172-019-2624-y

The paper presents the results concerning the use of the supercomputer docking program SOL-P, which performs a search for low-energy minima of protein—ligand complexes in the MMFF94 force field without using a grid of precalculated potentials for protein—ligand interactions. The SOL-P docking program can be applied to the generalized docking of ligands with a large number of internal rotational degrees of freedom (torsions). This program is based on a tensor train global optimization algorithm. The SOL-P program was successfully applied to the docking of oligopeptide ligands consisting of 3–6 amino acid residues and having 18–25 internal rotational degrees of freedom.