Research data from in silico analyses of the structural and electronic properties of α-/γ-aminobutyric acids and their interactions with Canavalia brasiliensis seed lectin.

Description

Data inputs from the in silico evaluation of the work entitled "The structural and electronic properties of α-/γ-aminobutyric acids and their interactions with Canavalia brasiliensis seed lectin.". The data correspond to the structures obtained by molecular docking, used to prepare the trajectories via CHARMM-GUI and executed in AMBER. Also included are the data used for the Density Functional Theory (DFT) calculation of the structural and electronic properties of the hormones α-/γ-aminobutyric acids (AABA/GABA). Finally, the script used for the entropy calculation by the "Interaction Entropy" method, from the data obtained by the calculation of binding free energy by MM-GBSA present in AMBERTOOLS, is also included.

Steps to reproduce

The .pdb files must be uploaded to the CHARMM-GUI web server to prepare the trajectories. Then, the data generated by the server must be used to process the dynamics via AMBER. The instructions and settings used are described in section 2.4 of the article to which this repository is associated. In the case of entropy calculation, We perform calculations of Interaction Entropy as described in Section 4.6 from article. The main idea is to obtain the output from Eq. 23, based on a Fortran 77 code called “entropylig.f” which evaluates the fluctuation of the energy terms in order to calculate the interaction entropy through Eq. 23. We followed these steps: 1. Define the number of simulation frames available using the parameter “fii” (line 19 of entropylig.f). The number of frames is given by the first column of the DELTA Energy Terms content in the Molecular Dynamics simulation output file. 2. Extract the column content “Delta G gas”, representing the protein-ligand binding free energy, from the Molecular Dynamics simulation output and save it in a blank file named “energlig.dat”. 3. Extract the column content “Delta G solv”, representing the solvation free energy, from the Molecular Dynamics simulation output and save it in a blank file named “enersolv.dat”. 4. Compile and run “entropylig.f”. We use the Intel Fortran compiler on a Linux distribution. In a terminal, we use “ifx entropylig.f” to compile, then “./a.out” to execute. 5. As final output files, we obtain “entropylig.txt”, which contains the interaction entropy as a function of time, and “medias.txt”, which includes the average of Delta G gas and its standard deviation, the average of interaction entropy, the average of Delta G solv and its standard deviation, and the final free energy.

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