4D-QSAR modeling program
This program base on LQTA-QSAR method.It can be used in the LINUX operating system.
For LQTA-QSAR, please cite:
J.P.A. Martins, E.G. Barbosa, K.F.M. Pasqualoto, M.M.C. Ferreira. J. Chem. Inf. Model. 2009, 49, 1428–1436.
E.G. Barbosa, M.M.C. Ferreira, Mol. Inf. 2012, 31, 75–84.
python >= 3
Gaussian >= 09
GaussianView
dos2unix
Acpype
AmberTools >= 2017
Gromacs >= 2018
OpenBabel
VMD
Put the QSAR KING package in any directory. Open the terminal at the directory, type:
$ mv QSAR_KING ~
$ sudo echo "~/QSAR_KING/files" >> $HOME/.bashrc
$ sudo chmod -R a+x ~/QSAR_KING/files/
$ python -m pip install --upgrade pip
$ pip install --upgrade numpy sklearn matplotlib
It contains all names of compounds,The text file will be:
m01
m02
m03
Each line of this file must contain the atom indexes from Gaussian that will be aligned, separeted by "tab". For example, the Gaussian atoms indexes of m01 and m02 that will be aligned are 1,3,5,7. For m03 these atoms have different Gaussian indexes, that are 2,4,5,9. The "index.txt" file will be:
1 3 5 7
1 3 5 7
2 4 5 9
If the "names.txt" file has a different order, the same order must beused in "index.txt" file
It contains the bioactive value (pIC50 value) of all compounds, corresponding to the name.txt. The text file will be:
3.2
5.4
6.1
It contains the name of the reference compound used in the alignment step. For example, m02 was chosen as the alignment reference. The text file will be:
m02
Manually specify which compounds are used as test sets. If there is no such file, the program will randomly pick one-fifth of the compounds as a test set. For example, m02 is in the test set and m01,m03 are in the training set, the text file will be:
m02
Put all *.log, *.gesp and *.txt files in a directory, open the terminal and navigate to that directory,type:
$ QSAR_KING
Wait until it done, your 4D_QSAR model will be built automatically by QSAR_KING!