Description

You are given with a target protein-protein complex (experimental) structure and a list of (computational) docking decoys generated by some docking techqniue for the same protein structure. Write a program (in C or C++ or Python laguage) that for each decoys will compute the Interface Area, LRMSD, IRMSD, Fnat and Solvation Energy.
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Sample Input/Output:
Download the attached zip file and unzip it. You will get one directory and three files:
File: target.pdb
Directory: Decoys
File: paper.pdf File: SI.pdf
target.pdb is the target protein dimeric complex structure file in PDB file format. There are two chains (column number 22) – A and B. Chain A is your receptor and Chain B is your ligand.
Using one docking algorithm, receptor and ligand was docked and the top 10 predictions as per the docking algorithm was scored and ranked. All of them are stored in Decoys directory.
You need to evaluate the goodness of the decoys by calculating the Interface Area, Solvation Energy, LRMSD, IRMSD, and Fnat score. Tabulate them as follows and store it as Score.txt file.
Filename | Interface Area | Solvation Energy | LRMSD | IRMSD | Fnat score ———————————————————————————————–complex1.pdb | complex2.pdb |
… …
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The detailed definitions of Interface Area, Solvation Energy, LRMSD, IRMSD, and Fnat score can be found in the pdf files as per following instructions.
Reference:
In the attached Journal paper paper.pdf you will get the definition of
(i) Interface Area (at page 2, under Interface Area sub-section),
(ii) LRMSD, IRMSD, Fnat (at page 4, under Evaluation Definitions subsection)
(iii) Solvation energy (page 2 under Solvation Energy subsection and at Table S1 of file SI.pdf).