TABA - Tool to Analyze the Binding Affinity

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.

Figure of a molecule and mass-spring
Protein-ligand as a mass-spring system. We used the atomic coordinates for the complex CDK2-roscovitine (PDB: 2A4L) (From Azevedo et al., 1997)

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 Download Taba Installer
  • 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 Download Taba compressed file
  • 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 Download Taba
  • 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 Download Taba
  • 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.


Figure Main window of Taba
Main window of Taba

To test:

To test Taba you can use the codes of this structure (CDK):

  • Molecule Type: protein
  • Experimental Method: X-RAY
  • Binding Affinity: Affinity Type is Ki
  • Enzyme Classification Search : EC 2.7.11.22
  • Codes to copy/paste:
1E1V, 1E1X, 1H1S, 1JSV, 1OGU, 1PXM, 1PXN, 1PXO, 1PXP, 1PYE, 1V1K, 2CLX, 2EXM, 2FVD, 2XMY, 2XNB, 3BLR, 3DDQ, 3LFN, 3LFS, 3MY5, 4ACM, 4BCK, 4BCM, 4BCN, 4BCO, 4BCP, 4BCQ, 4EOP, 4NJ3, 5D1J

What Taba Means

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.

Figure of a taba
Website figure: http://www.dicasdamel.com.br

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.
Taba was developed by Amauri Duarte and Prof. Dr. Walter Filgueira de Azevedo Jr.