The introduction and overview of Fast Amber Rescoring for PPI inhibitors (farPPI) websever is available at “Home” page. In addition, the status of server is monitored on this page.

Job submission

A rescoring job can be submitted on the “Submit” page by clicking the “Submit” button when correct (1) Project name , (2) Docked pose file, (3) Receptor file, (4) Force field, and (5) Rescoring procedure are provided.

Job monitoring and result downloading

After a job is successfully submitted, the detailed information about it can be observed on the “Queue” page. When the calculation is done, a link for the corresponding result will be generated for downloading.

Datasets downloading

The ready-to-dock and ready-to-rescore benchmark datasets can be download on the “Download” page by clicking the corresponding links.

Tutorial for rescoring docking poses locally with MM/GB(PB)SA methods

In you need to rescoring docking poses locally which a workflow similar to farPPI, below is a concise and practical tutorial for you. Before you start this tutorial please download the material that will be used in this tutorial tutorial.zip.

Program version requirements: AmberTools/Amber 17 or higher, Python 2.7.14 or higher with matplotlib and seaborn libraries.

Step1: System preparation

Input: protein.pdb, poses.mol2

Output: complex_solv_radii.prmtop, complex_solv_radii.inpcrd

Script: step1_preparation.py with 5 position parameters pose_file receptor_file gaff|gaff2 ff99SB|ff14SB all|pb1|pb3|pb4|gb1|gb2|gb5|gb6

tar xvf tutorial.tar.gz
cd work/step1_preparation
python ../../script/step1_preparation.py ../../structure/poses.mol2 ../../structure/protein.pdb gaff2 ff14SB all

Step2: complex minimization

Input: complex_solv_radii.prmtop, complex_solv_radii.inpcrd

Output: min3.restrt

Script: step2_minimization.py with 2 position parameters preparation_dir all|pb1|pb3|pb4|gb1|gb2|gb5|gb6

cd ../step2_minimization
python ./../script/step2_minimization.py ../step1_preparation all

Step3: MM/GB(PB)SA rescoring

Input: complex.pdb, complex_solv_radii.prmtop, complex_radii.prmtop, receptor_radii.prmtop, ligand_radii.prmtop, min3.restrt

Output: mm_pbsa_statistics.out

Script: step3_rescoring.py with 3 position parameters preparation_dir receptor_file all|pb1|pb3|pb4|gb1|gb2|gb5|gb6

cd ../step3_rescoring
python ../../script/step3_rescoring.py ../step1_preparation ../../structure/protein.pdb all

Step4: Data visualization

Input: mm_pbsa_statistics.out

Output: rescoring_result.csv, rescoring_result.pdf

Script: step4_visualization.py with 1 position parameter rescoring_dir

cd ../step4_visualization
python ../../script/step4_visualization.py ../step3_rescoring