🧬 Protein-InDelMaker

Developed at Prof. Costas Maranas Lab at The Pennsylvania State University by Veda Sheersh Boorla

📧 Any bugs/comments/questions to be addressed to: [email protected]

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📖 Citation

If you use this package, please cite the following article. Thanks!

@article{Chowdhury2020,
  author = {Chowdhury, R. and Grisewood, M.J. and Boorla, V.S. and Yan, Q. and Pfleger, B.F. and Maranas, C.D.},
  title = {IPRO+/−: Computational Protein Design Tool Allowing for Insertions and Deletions},
  journal = {Structure},
  year = {2020}
}

🛠️ Requirements

Make sure your system has these installed before running the package:

1. Python 3.7 and above
2. PyRosetta version 4 for Python 3.7 (Download here)
3. Numpy version 1.16 and above

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📂 Input Files Preparation

The package needs two input files:

1. .pdb file of the protein to be modeled (as per RCSB format).
2. .input file specifying the list of modifications to make (format described below).

Guidelines for .input File

• Each line of the file may start with any of the three keywords:
  {INSERT, DELETE, MUTATE}
• Following a keyword, specify the chain in the format:
  CHAIN_X
  where X is the alphabet corresponding to the chain that needs to be modified.
• After the chain specification, list the modifications.

Example Scenarios

Scenario 1: Delete residues 14, 15, 16 from CHAIN_A.
Input file:

DELETE CHAIN_A 14-16

or equivalently

DELETE CHAIN_A 14,15,16

Scenario 2: Insert the stretch of residues PPP after residue 20 in CHAIN_A.
Input file:

INSERT CHAIN_A 20_PPP

Scenario 3: Replace residues 5, 6, 7 of CHAIN_A with G, L, A respectively.
Input file:

MUTATE CHAIN_A 5_G,6_L,7_A

Scenario 4: Combine the above modifications.
Input file:

DELETE CHAIN_A 14-16 INSERT CHAIN_A 20_PPP MUTATE CHAIN_A 5_G,6_L,7_A

• Note: All numbering follows the original PDB numbering to avoid ambiguity!

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🧠 Algorithm

• Chain breaks formed by insertions and deletions are closed using the KIC loop closure algorithm as implemented in Rosetta.
• Loop closure is followed by all-atom Rosetta relax in Cartesian coordinates and gradient-based minimization in Cartesian coordinates.
• Mutations are modeled as amino-acid substitutions followed by all-atom relax and gradient-based minimization.

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🚀 Running a Demo

Navigate to the root directory of InDelMutator in a shell and run the following command:

python main.py demo demo.pdb demo.input

After the run is complete (which could take a few minutes), you should see your results in ./results/demo/

To read the help about possible arguments to main.py, run

python main.py -h

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📊 Results

• A result.pdb file will be output after all modifications of every line in the input file have been applied.
  For example, if the input file contains three lines (as in Scenario 4 above), the results folder will have result_1.pdb, result_2.pdb, and result_3.pdb.
• A result.txt file will be output, containing the Rosetta scores. For example:

0 -230.1
1 -233.3
2 -220.3
3 -210.9

• First row: Rosetta score of the input structure.
• Second row: Rosetta score after applying modifications from input line 1.
• Third row: Rosetta score after applying modifications from input lines 1 and 2.
• Fourth row: Rosetta score after applying modifications from input lines 1, 2, and 3.

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⚠️ Limitations

1. Insertions and deletions work only on residues that are at least 3 residues away from both the N and C terminus.

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✅ Fixed Issues

1. Including non-protein molecules is now possible. An additional .params file is needed, prepared as described here.

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🆕 Added Functionality

1. 28th November, 2022 - Added argparse functionality.

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🐛 Known Issues

1. Fails if the PDB file has non-integer residue numbers (e.g., 12B).
   Workaround: Modify the PDB file so that all residue numbers are integers. A script clean_pdb.py is provided in ./scripts/ for this purpose.

2. The accuracy of the package generally drops with the number of insertions or deletions due to the cumulative effect. See the IPRO+/- publication for a benchmark on reproducing crystal structures of indel variants of antibodies.