Molecular docking data preparation tool

V. O. Samarskaya; A. V. Kovalenko; G. A. Sroslova; M. V. Postnova; A. A. Shiroky; A. G. Serov

doi:10.1117/12.2522533

3 June 2019 Molecular docking data preparation tool

V. O. Samarskaya, A. V. Kovalenko, G. A. Sroslova, M. V. Postnova, A. A. Shiroky, A. G. Serov

Proceedings Volume 11067, Saratov Fall Meeting 2018: Computations and Data Analysis: from Nanoscale Tools to Brain Functions; 110670S (2019) https://doi.org/10.1117/12.2522533
Event: International Symposium on Optics and Biophotonics VI: Saratov Fall Meeting 2018, 2018, Saratov, Russian Federation

Abstract

Bioinformation data capturing and preprocessing for molecular modelling is exceptionally time-consuming task. Researcher forced to use inconsistent instruments, which are generate vast amounts of diverse-structured data. Here we propose an integrated instrument automating the stage of data pre-processing for molecular docking – searching of protein receptors, their spatial structures and suitable ligands. The algorithm automatically finds all the synonymic constructs of original query, requesting specified biological databases, populating the list of receptor’s and their ligands’ PDB-identifiers and converts them to AutoDock format (PDBQT). The data sources are open-access specialized biological databases – UniProtKB, Protein Data Bank (PDB) and ZINC15. The virtual screening algorithm implemented using the Python 2.7.9 programming language with several plug-in modules. The result is the data preparation tool for further use in AutoDock-family docking software. The tool has two variants of user interface – desktop application and chatbot for the Telegram messenger.

Citation Download Citation

V. O. Samarskaya, A. V. Kovalenko, G. A. Sroslova, M. V. Postnova, A. A. Shiroky, and A. G. Serov "Molecular docking data preparation tool", Proc. SPIE 11067, Saratov Fall Meeting 2018: Computations and Data Analysis: from Nanoscale Tools to Brain Functions, 110670S (3 June 2019); https://doi.org/10.1117/12.2522533

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