ITScoreAff

ITScoreAff is an iterative knowledge-based scoring function for protein-ligand interactions by considering binding affinity information. Its is an improved version of the iterative knowledge-based scoring function ITScore by considering binding affinity information

Copyright © 2023 Xuejun Zhao, Hao Li, Sheng-You Huang and Huazhong University of Science and Technology

ITScoreAff is freely available for academic or non-commercial users.

Click ITScoreAff_v1.0 to directly download the program.

For commercial license of ITScoreAff, please contact us at huangsy@hust.edu.cn.

If you have any questions regarding ITScoreAff, please contact us at huangsy@hust.edu.cn.

How to install ITScoreAff

Required system: CentOS 7.0 or newer

ITScoreAff does not depend on any other software. The installation of ITScoreAff is very simple. Just copy the package anywhere and directly run it like it.

        tar -xzf ITScoreAff_v1.0.tar.gz
        cd ITScoreAff_v1.0
        ./ITScoreAff

How to run ITScoreAff

The usage of ITScoreAff is as follows:

        Usage: receptor_MOL2_file  ligand_MOL2_file

where "receptor_MOL2_file" is the protein structure in mol2 format, and "ligand_MOL2_file" is the ligand binding mode file in mol2 format that may contains one or multiple binding modes.

Example usage:

        cd example
        ../ITScoreAff 4llx_protein.mol2 4llx_decoys.mol2

Then, you will get the calculated scores like this

 num_ligand   id_ligand        ITScoreAFF
     1       4llx_208          -37.51751
     2       4llx_213          -39.64339
     3       4llx_236          -41.56639
     4       4llx_243          -16.24060
     5       4llx_247          -15.67570
     6       4llx_276          -40.07759
     7       4llx_293          -44.00158
     8       4llx_302          -38.94650
     9       4llx_386          -42.76110
    10       4llx_402          -32.96050
   ......

Reference(s):

1. Xue-jun Zhao, Hao Li, Sheng-You Huang. An iterative knowledge-based scoring function for protein-ligand interactions by considering binding affinity information, 2023.

2. Huang SY, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J Comput Chem. 2006;27(15):1866-75.

3. Huang SY, Zou X. An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem. 2006;27(15):1876-82.