Razvoj računalniškega grafičnega vmesnika v programu PyMOL za strukturno in na osnovi-liganda podprto načrtovanje zdravil

Jurić, Vito (author), Gobec, Stanislav (mentor), Konc, Janez (comentor)

Vtičniki za in silico razvoj zdravil LiSiCA GUI, ProBiS H2O in ProBiS H2O MD so vtičniki za program PyMOL. PyMOL je eno najbolj razširjenih orodij za 3D molekularno vizualizacijo. Z zadnjimi nadgradnjami programa PyMOL so se spremenile zahteve za vtičnike, kot so sprememba zahtevanega programskega jezika iz Python 2 v Python 3 in sprememba osnove za grafični uporabniški vmesnik iz Tcl/Tk v PyQt. Te spremembe v zahtevah pomenijo, da vtičnikov LiSiCA GUI, ProBiS H2O in ProBiS H2O MD ni več mogoče zagnati in uporabljati. Odločili smo se, da jih prepišemo v skladu z zahtevami programa PyMOL in jim dodamo nove funkcije, kjer je to smiselno. Z LiSiCA GUI vtičnikom se tako lahko spet izvaja in silico 2D in 3D rešetanje na podlagi Tanimotovega indeksa; z vtičnikom ProBiS H2O je ponovno omogočena analiza ohranjenih vod na strukturi analiziranega proteina glede na strukture podobnih proteinov; z vtičnikom ProBiS H2O MD pa je usposobljena analiza ohranjenih vod na strukturi analiziranega proteina glede na spreminjane 3D strukture tekom trajektorije, dobljene z molekulsko dinamiko tega proteina. Za poenotenje vtičnikov LiSiCA GUI, ProBiS H2O in ProBiS H2O MD smo razvili tudi nov vtičnik InsilabGUI, ki vsebuje te vtičnike, kar olajša in poenostavi njihovo namestitev in medsebojno uporabo za in silico razvoj.

• Language: Slovenian
• Keywords: In silico, PyMOL, grafični uporabniški vmesnik, virtualno rešetanje, ohranjena voda
• Work type: Master's thesis/paper
• Organization: FFA - Faculty of Pharmacy
• Year: 2021
• PID: 20.500.12556/RUL-132949
• Publication date in RUL: 07.11.2021

Secondary language

• Language: English
• Title: Development of a computer graphical interface within the PyMOL programme for structure and ligand-based drug design

Abstract

The plugins for in silico drug development LiSiCA GUI, ProBiS H2O and ProBiS H2O MD are plugins for the PyMOL program. PyMOL is one of the most widely used tools for 3D molecular visualization. With recent updates to PyMOL, the requirements for its plugins have changed, which are the change of the required programming language from Python 2 to Python 3 and the change of the required graphical user interface toolkit from Tcl/Tk to PyQt. Due to these changes, it is not possible to run and use the LiSiCA GUI, ProBiS H2O and ProBiS H2O MD plugins. We have decided to rewrite them per PyMOL’s requirements and add new features where appropriate. With the LiSiCA GUI plug-in, both in silico 2D and 3D virtual screening, based on the Tanimoto index, can be performed again; with the ProBiS H2O plug-in, the analysis of preserved waters on the structure of an analysed protein with respect to the structures of similar proteins is again enabled; with the ProBiS H2O MD plug-in, the analysis of preserved waters on the structure of an analysed protein with respect to the changed 3D structures during a trajectory, obtained by the molecular dynamics of this protein, is possible. To unify the LiSiCA GUI, ProBiS H2O and ProBiS H2O MD plug-ins, we have also developed a new InsilabGUI plug-in that contains these three plug-ins, which facilitates and simplifies their installation and mutual use for in silico development.

• Keywords: In silico, PyMOL, graphical user interface, virtual screening, conserved water