APE-Gen: Anchored Peptide-MHC Ensemble Generator

Description:

• APE-Gen is a tool that generates multiple clash-free conformations of a peptide bound to an MHC

• All that is required for input is the sequence of the peptide and the MHC allotype name (if supported)

• Minimal example: python APE_Gen.py QFKDNVILL HLA-A*24:02

• For a peptide with "n" residues, APE-Gen will use a template of another peptide with "n" residues to place the anchor residues in the correct pocket of the MHC

  • to change the template, modify n-mer-templates.txt for the corresponding n-mer, then add the template pdb file (peptide and MHC) to the templates/ folder

• A receptor model is also needed to run APE-Gen

  • if the allotype of the MHC is supported (found in receptor-class-templates.txt), then simply specify the name as input into APE-Gen
  • if the allotype is not supported, but one has the PDB file of the receptor
    • place the PDB file inside the templates/ folder
    • modify receptor-class-templates.txt with an appropriate name
    • then call APE-Gen with the chosen name
  • One way to obtain a model of the receptor is to use the provided scripts in modeller_scripts/ for homology modelling (see below)

• PDB File preparation:

  • For PDB files to be used as input anywhere in the script, the chains must be labelled in a particular way
  • chain A is the heavy alpha chain, chain B is the light beta-immunoglobulin chain, chain C is the peptide

• Specifying receptor degrees-of-freedom

  • modify flex_res.txt to add/remove residues that are allowed to be flexible during the SMINA minimization step

• dunbrack.bin and loco.score are files required for the RCD step

• align.py is required for using PYMOL for alignment of PDB files

• minimize.py is needed for further minimization using OpenMM

Output

• Each round of APE-Gen is saved within a folder with the index of the round (counting from 0)

• full_system_confs/ contains the ensemble of conformations of peptide and MHC after energy refinement and filtering

  • each conformation is named by the index of the loop as generated by RCD
    • not every conformation makes it past the energy refinement and filtering step

• peptide_confs.pdb contains only the peptide conformations

• filtered_energies.npz is a numpy file that contains the energies of the ensemble according to the SMINA scoring function

  • it contains two arrays of the same size: filtered_indices which contains indices of each conformation and filtered_energies which contains the corresponding energies

Helper scripts

• get_pMHC_pdb.py

  • usage: python get_pMHC_pdb.py <pdb code>
  • assumes pdb code is of a peptide-MHC structure
  • adds missing atoms/residues, removes all waters and ions, labels chains as A,B,C where chain C is the peptide

• mutate.py

  • Usage: ~/pymol/bin/pymol -qc mutate.py <pdb> <selection> <new_residue in 3-letter code> <name of new pdb file>
  • example: ~/pymol/bin/pymol -qc mutate.py 0.pdb C/1/ ALA 0_mutated.pdb

Options help:

usage: APE_Gen.py [-h] [-n NUM_CORES] [-l NUM_LOOPS] [-t RCD_DIST_TOL] [-r]
                  [-d] [-p] [-a ANCHOR_TOL] [-o] [-g NUM_ROUNDS]
                  [-b {receptor_only,pep_and_recept}] [-s] [--use_gpu]
                  [--no_progress] [--clean_rcd]
                  peptide_input receptor_class

Anchored Peptide-MHC Ensemble Generator

positional arguments:
  peptide_input         Sequence of peptide to dock or pdbfile of crystal
                        structure
  receptor_class        Class descriptor of MHC receptor. Use REDOCK along
                        with crystal input to perform redocking. Or pass a PDB
                        file with receptor

optional arguments:
  -h, --help            show this help message and exit
  -n NUM_CORES, --num_cores NUM_CORES
                        Number of cores to use for RCD and smina computations.
                        (default: 8)
  -l NUM_LOOPS, --num_loops NUM_LOOPS
                        Number of loops to generate with RCD. (Note that the
                        final number of sampled conformations may be less due
                        to steric clashes. (default: 100)
  -t RCD_DIST_TOL, --RCD_dist_tol RCD_DIST_TOL
                        RCD tolerance (in angstroms) of inner residues when
                        performing IK (default: 1.0)
  -r, --rigid_receptor  Disable sampling of receptor degrees of freedom
                        specified in flex_res.txt (default: False)
  -d, --debug           Print extra information for debugging (default: False)
  -p, --save_only_pep_confs
                        Disable saving full conformations (peptide and MHC)
                        (default: False)
  -a ANCHOR_TOL, --anchor_tol ANCHOR_TOL
                        Anchor tolerance (in angstroms) of first and last
                        backbone atoms of peptide when filtering (default:
                        2.0)
  -o, --score_with_openmm
                        Rescore full conformations with openmm (AMBER)
                        (default: False)
  -g NUM_ROUNDS, --num_rounds NUM_ROUNDS
                        Number of rounds to perform. (default: 1)
  -b {receptor_only,pep_and_recept}, --pass_type {receptor_only,pep_and_recept}
                        When using multiple rounds, pass best scoring
                        conformation across different rounds (choose either
                        'receptor_only' or 'pep_and_recept') (default:
                        receptor_only)
  -s, --min_with_smina  Minimize with SMINA instead of the default Vinardo
                        (default: False)
  --use_gpu             Use GPU for OpenMM Minimization step (default: False)
  --no_progress         Do not print progress bar (default: False)
  --clean_rcd           Remove RCD folder at the end of each round (default:
                        False)

Installation instructions:

1. install miniconda

• https://conda.io/miniconda.html

2. using conda, install the following

• conda install -c bioconda smina
• conda install -c omnia pdbfixer
• conda install -c conda-forge mdtraj
• conda install -c schrodinger pymol
• conda install -c bioconda autodock-vina
• conda install -c omnia -c conda-forge openmm

3. install RCD (v1.40)

• http://chaconlab.org/modeling/rcd/rcd-download
• make sure RCD is added to path so that rcd is a command in the terminal
• intel mkl may be needed (conda install -c intel mkl) and added to library path

Using Modeller script

usage: model_receptor.py [-h] [-n NUM_MODELS] alpha_chain_seq template

Homology Modeling of HLAs using Modeller

positional arguments:
  alpha_chain_seq       Fasta file (.fasta) containing the sequence of the
                        alpha chain of HLA or name of HLA allele (ex.
                        HLA-A*02:01). If allele name given, the program will
                        try to download the sequence from EMBL-EBI.
  template              PDB of the template HLA or name of HLA allele (ex.
                        HLA-A*02:01). If allele name given, a template based
                        on the allele's supertype (as defined in
                        supertype_templates.csv) will be chosen.

optional arguments:
  -h, --help            show this help message and exit
  -n NUM_MODELS, --num_models NUM_MODELS
                        Number of models to sample with Modeller (default: 10)

• Requires Modeller, Biopython, and BeautifulSoup4
  • conda install -c salilab modeller
  • conda install -c conda-forge biopython
  • conda install -c anaconda beautifulsoup4
  • conda install -c anaconda requests
• Model with the best DOPE score is found in best_model.pdb
• Example: python model_receptor.py P01892.fasta 3I6L.pdb
  • Requires license key
  • models HLA-A*02:01 using 3I6L as a template
    • 3I6L contains a model of HLA-A*24:02
• Even simpler example: python model_receptor.py HLA-A*02:01 HLA-A*02:01
  • First argument says that the sequence of HLA-A*02:01 will be downloaded
  • Second argument says that a template PDB will be downloaded based on a representative allele from the same supertype classification

Instructions to run Minimal Example with Docker

• Open a Terminal
• Pull image from Docker hub: docker pull jayab867/apegen:v2.0
• Go to the directory where you would like the APE-Gen results to be saved
• Create a container that links the current working directory to a directory in the container called /data
  • docker run -it --rm -v $(pwd):/data --workdir "/data" jayab867/apegen:v2.0
• Run APE-Gen: python /APE-Gen/APE_Gen.py QFKDNVILL HLA-A*24:02
• Exit the container with Ctrl-D
• There will be a number of folders which contain the results for each round of APE-Gen
  • Default is one round: so a single folder in this example called 0/
  • In each folder:
    • The best scoring conformation for each round is called min_energy_system.pdb
    • The whole ensemble generated is located in full_system_confs/