Modeling disordered protein interactions from biophysical principles
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idp_relax.inp

README.md

IDP-LZerD

IDP-LZerD models the bound conformation of a disordered PPI, where one intrinsically disordered protein (IDP) binds to an ordered protein. The inputs are the sequence of a disordered protein and the structure of an ordered protein.

Copyright (C) 2016-2017 Lenna X. Peterson, Daisuke Kihara, and Purdue University.

License: GPL v3 for academic use. (For commercial use, please contact us for different licensing)

Contact: Daisuke Kihara (dkihara@purdue.edu)

Reference: Lenna Peterson, A Roy, C Christoffer, G Terashi, and D Kihara. (2017) Modeling disordered protein interactions from biophysical principles. PLoS Computational Biology 13: e1005485. doi: 10.1371/journal.pcbi.1005485

Installation

To run the test, LZerD and all Python dependencies are required.

Python dependencies

  • apsw
  • numpy
  • scipy
  • pandas
  • Biopython

Binary dependencies

Getting started

  1. Edit PATHS.ini to specify path to LZerD, blastpgp, nr, and Rosetta

Test protein

  1. Edit 'test/test_decoys.sh' to specify path to IDP-LZerD
  2. Run test (NOTE: creates ~250 GB of files): cd test && ./test_decoys.sh
  3. Non-refined paths will be output in 'test/4ah2ac3'
  4. Follow standard procedures to prepare PDB files for CHARMM
  5. Edit CHARMM input file 'idp_relax.inp' to run CHARMM

Running a new protein

  1. Prepare FASTA sequence of IDP and structure of ordered partner protein
  2. Create fragments with Rosetta using rosetta_tools/fragment_tools/make_fragments.pl and the flags '-frag_sizes 9 -n_frags 30'
  3. Convert Rosetta output to PDB format using 'scripts/rosetta_to_pdb.py'
  4. Rename 'window_data.csv' to '${PDBID}_data.csv'
  5. Convert CA to full-atom backbones using Pulchra
  6. Build side-chains using chosen side-chain modeling software
  7. Put fragments into subdirectories as in 'test/4ah2'
  8. Run LZerD on each fragment
  9. Score LZerD output using GOAP and ITScorePro
  10. Copy and edit 'test/test_decoys.sh' for new protein and run as for test protein