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Szczepaniak, Oskar, 2025, "Interaction of selected plant secondary metabolites with Ap3A and Ap4A dinucleotide cell regulators", https://doi.org/10.18150/A9UMDZ, RepOD, V1
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[PL:]
Przedmiotowy zbiór danych zawiera wyniki modelowania oddziaływań wybranych związków fenolowych oraz stilbenów z dwoma nukleotydowymi regulatorami cyklu komórkowego: Ap3A oraz Ap4A, a także ich energie interakcji.
Cząsteczki zostały wstępnie zdokowane do modeli regulatorów z wykorzystaniem programu Autodock Nova. Wybrano predykcje o największej wartości powinowactwa wiązania (ang. binding affinity) z 8 proponowanych przez program do wyznaczenia energii interakcji. W przypadku predykcji o podobnych lub identycznych wartościach powinowactwa wybierano kilka modeli do badań z oznaczeniem kolejnych var_2 - var_4.
Obliczenia energii interakcji wykonano z wykorzystaniem programu Gaussian 09 metodą Hartree-Focka. Stosowano bazy funkcyjne 3-21G (brak opisu bazy w nazwie), a następnie stosując pliki kontrolne z obliczeń tą bazą jako plik inputu dokonywano obliczeń bazą 3-21G*, 6-31G, oraz na końcu 6-31G(d). Dla pozostałych stosowanych baz, pliki wyjściowe w formacie .log zawierają nazwę przyrostek odnoszący się do baz funkcyjnych, odpowiednio _1 dla 3-21G*, _2 dla 6-31G oraz _3 dla bazy 6-31G(d). Energie oddziaływań obliczono wykorzystując funkcję programu counterpoise.
[ENG:]
The data set contains the results of interactions modeling between selected phenolic compounds and stilbenes with binucleotide cell-cycle regulators: Ap3A and Ap4A, as well as their interaction energies.
The molecules were initially docked to the regulator models using the Autodock Nova program. For each model one prediction with the highest binding affinity value was selected out from 8 proposed by the program to determine the interaction energy. In the case of predictions with similar or identical binding affinity values, several models were selected for testing with the subsequent var_2 - var_4 descriptions in the file title.
The interaction energy was calculated using the Gaussian 09 program using the Hartree-Fock method. The 3-21G function bases were used (no base description in the name), and then, using control files of calculations using this function base as input files, deepened calculations were made using the 3-21G*, 6-31G, and finally 6-31G(d) bases. For the extended bases used, the output files in .log format contain suffixes _1, _2, and _3, respectively. Interaction energies were calculated using the counterpoise function.
ab initio, dinucleotide regulators, stilbenes, phenolic compounds
2026-09-30
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