maranasgroup / Protein-InDelMaker

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 [e-mail]

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

Chowdhury, R., Grisewood, M.J., Boorla, V.S., Yan, Q., Pfleger, B.F. and Maranas, C.D., 2020. IPRO+/−: Computational Protein Design Tool Allowing for Insertions and Deletions. Structure.

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 (http://www.pyrosetta.org/dow)
3. Numpy version 1.16 and above

Input files preparation: The package needs two input files:

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

Guidelines for .input file:-

• Each line of the file may start with any of the three key-words: {INSERT, DELETE, MUTATE}

• Following a key-word has to be the chain specification in the format: CHAIN_X where X is the alphabet corresponding to the chain that needs to be modified

• Following the chain specification, list of modifications have to specified.

• Consider the following scenarios and input files prepared

  Scenario 1: It is required to delete residues 14,15,16 from CHAIN_A and only the structure resulting from the three deletions is of interest. Then the input file will contain the following line:

  DELETE CHAIN_A 14-16

  or in an equivalent form

  DELETE CHAIN_A 14,15,16

  Scenario 2: It is required to insert the stretch of residues 'PPP' after residue 20 in CHAIN_A. Then the input file will contain the following line:

  INSERT CHAIN_A 20_PPP

  Scenario 3: It is required to replace the residues 5,6,7 of CHAIN_A with G,L,A respectively. Then the input file will contain the following line:

  MUTATE CHAIN_A 5_G,6_L,7_A

  Scenario 4: It is required to do the modifications of three above scenarios to one pdb. Then the input file will contain the following lines:

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

• Note that all the numbering follows the original pdb numbering provided as input to avoid ambiguity!

Algorithm: Chain breaks formed by insertions and deletions are closed using KIC loop closure algorithm as implemented in Rosetta. The 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.

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

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

Results:

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

• A result.txt file will be output which has the rosetta scores. For example,

  First row will have the rosetta score of input structure Second row will have the rosetta score of structure obtained after applying modifications of input line 1 Third row will have the rosetta score of structure obtained after applying modifications of input line 1 and 2 Third row will have the rosetta score of structure obtained after applying modifications of input line 1, 2 and 3

  For the example in above line, this file will contain four rows like below:

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

Limitations:

1.Insertions and Deletions work only on residues which are at least 3 residues away from both N and C terminus.

FIXED

1. Including non-protein molecules is now possible. The additional input file needed is a .params file that needs to be prepared as descirbed here:- https://www.rosettacommons.org/demos/latest/tutorials/prepare_ligand/prepare_ligand_tutorial

ADDED FUNCTIONALITY

1. 28th November, 2022 - Added argparse functionality

Known issues: 1.Fails if pdb file has non integer residue numbers For example, '12B' A get around for this issue is to modify the pdb file first so that all of the residue numbers are integers. A script 'clean_pdb.py' from rosetta tools has been 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.