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.

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.

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.

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

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