Supercomputer docking with a large number of degrees of freedom

Docking represents one of the most popular computational approaches in drug design. It has reached popularity owing to capability of identifying correct conformations of a ligand within an active site of the target-protein and of estimating the binding affinity of a ligand that is immensely helpful...

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Bibliographic Details
Published in:SAR and QSAR in environmental research 2019-10, Vol.30 (10), p.733-749
Main Authors: Sulimov, A., Kutov, D., Ilin, I., Zheltkov, D., Tyrtyshnikov, E., Sulimov, V.
Format: Article
Language:English
Subjects:
Algorithms
Atomic properties
Catalytic Domain
Computer applications
Computers - classification
Degrees of freedom
Docking
drug design
Drug development
Genetic algorithms
Global optimization
Ligands
Molecular Docking Simulation
Molecular modelling
Oligopeptides
Oligopeptides - chemistry
protein moveable atoms
Proteins
Software
Supercomputers
tensor train
Tensors
Visual observation
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Summary:Docking represents one of the most popular computational approaches in drug design. It has reached popularity owing to capability of identifying correct conformations of a ligand within an active site of the target-protein and of estimating the binding affinity of a ligand that is immensely helpful in prediction of compound activity. Despite many success stories, there are challenges, in particular, handling with a large number of degrees of freedom in solving the docking problem. Here, we show that SOL-P, the docking program based on the new Tensor Train algorithm, is capable to dock successfully oligopeptides having up to 25 torsions. To make the study comparative we have performed docking of the same oligopeptides with the SOL program which uses the same force field as that utilized by SOL-P and has common features of many docking programs: the genetic algorithm of the global optimization and the grid approximation. SOL has managed to dock only one oligopeptide. Moreover, we present the results of docking with SOL-P ligands into proteins with moveable atoms. Relying on visual observations we have determined the common protein atom groups displaced after docking which seem to be crucial for successful prediction of experimental conformations of ligands.
ISSN:1062-936X
1029-046X
DOI:10.1080/1062936X.2019.1659412