da Silva AD, Bitencourt-Ferreira G, de Azevedo WF Jr. Taba: A Tool to Analyze the Binding Affinity. J Comput Chem. 2019 doi: 10.1002/jcc.26048. PubMed
What is
Taba is a computational tool for the development of machine-learning
models to predict the affinity between ligands and proteins.
Taba uses information extracted from the three-dimensional structures
of protein-ligand complexes.
About the tool
Computational methods to evaluate protein-ligand interactions exert
great beneficial impact on the early stages of drug-design and
development. Although much development in this field has been achieved,
there is room for further progress in the creation of protein-targeted
scoring functions for calculation of ligand binding affinity. It was with this
in mind that we propose here a new computational tool to create machine-
learning models to calculate ligand-binding affinity. The computational tool
is called Taba, an acronym for tool to analyze the binding affinity.
Taba is an open source software and makes use of algorithms of supervised
machine learning such as least absolute shrinkage and selection operator
(Lasso) and elastic net to create a scoring function aimed to be used for a
specific protein family. Taba was developed using Python programming
language and makes use of scientific computing libraries such as NumPy,
SciPy, Matplotlib, and Scikit-learn. Taba calculates the average interatomic
distances between pairs of atoms involving protein and ligand using
atomic coordinates stored in protein data bank (PDB) files.
How to install Taba
You need to have Python 3.5 or 3.6 installed on your computer to run Taba. In addition, you also need NumPy (1.14.5*), Matplotlib, scikit-learn (0.19.1*), pyqt4 and SciPy (1.1.0*). *You can use a higher version as well.
To have Python and the libraries more easily, you can install Anaconda
in the following versions*:
Anaconda3-4.1.0-Windows-x86 (Windows 32-bit)
Anaconda3-4.1.0-Windows-x86_64 (Windows 64-bit)
*Use specifically the versions indicated above
Attention: If you already have a version of Taba installed, before making an update it is important to save the current experiment in Manage Experiments.
Installer for Windows 64 bits (from Google Drive)
Step 1. Download Taba Installer from Google Drive
Step 2. Just install: It is not necessary to configure the environment as described above
Installer for Linux 64 bits (from Google Drive)
Step 1. Download the Taba compressed file from Google Drive
Step 2. Just unzip the TabaLinux.zip file to your preferred folder: It is not necessary to configure the environment as described above
Step 3. Only in the first time: open the linux terminal and go to your preferred folder. So, type ./Taba. This will run Taba and create a short cut in yor work space
For all versions of windows
Step 1. Download Taba from GIT
Step 2. Unzip the zipped file ("TABA_dist.zip")
Step 3. Copy "TABA_dist" directory to c:\
Step 4. Open a command prompt window (Terminal) and type: cd c:\TABA_dist
then type: python taba.py
This launches GUI window for Taba. That´s it, good Taba session.
See help for additional information about how to run Taba.
For all versions of Linux
Step 1. Download Taba from GIT
Step 2. Unzip the zipped file ("TABA_dist.zip")
Step 3. Copy "TABA_dist" directory to your personal directory
Step 4. Open a terminal and type cd /your personal directory/TABA_dist
then type: python taba.py
This launches GUI window for Taba. That´s it, good Taba session.
See help for additional information about how to run Taba.
To test:
To test Taba you can use the codes of this structure (CDK):
Taba is an acronym for Tool to Analyze the Binding Affinity. In Portuguese, the name Taba means an indigenous village, where the dwellings of the Indians are located.
License
Taba is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.