The original implementation of methodology described in "Parapred: antibody paratope prediction using convolutional and recurrent neural networks" by Liberis et al.
Requirements:
To install:
python setup.py install in the root directory. If you are using a Python installation
manager, such as Anaconda or Canopy, follow their package installation instructions.pip install -r requirements.txt.parapred executable on the command line (run
parapred --help to check).requirements.txt and try executing python -m parapred --help or ./parapred-runner.py --help
in the root of this repository.➜ ~ parapred --help
Parapred - neural network-based paratope predictor.
Parapred works on parts of antibody's amino acid sequence that correspond to the
CDR and two extra residues on the either side of it. The program will output
binding probability for every residue in the input. The program accepts two
kinds of input (see usage section below for examples):
(a) The full sequence of a VH or VL domain, or a larger stretch of the sequence
of either the heavy or light chain comprising the CDR loops. (requires the
additional module anarci for Chothia numbering of sequences, available at
http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php).
Command example: `parapred seq DIEMTQSPSSLSASVGDRVTITCR...`
(b) A fasta file with various antibody sequences, either light or heavy chains
(requires anarci http://opig.stats.ox.ac.uk/webapps/sabdab-sabpred/ANARCI.php)
(c) A Chothia-numbered PDB file together with antibody's heavy and light chain
IDs (provided using `--abh` and `--abl` options). The program will overwrite
the B-factor value in the PDB to a residue's binding probability.
Multiple PDB files can be processed by specifying a description file (using
the `--pdb-list` option), which is a CSV file containing columns `pdb`,
`Hchain` and `Lchain` meaning PDB file name (.pdb extention will be appended
if missing), heavy chain ID and light chain ID respectively. For example:
pdb,Hchain,Lchain
2uzi,H,L
4leo,A,B
Extra columns in the CSV file are allowed and will be ignored. A folder
containing PDB files can be specified using the `--pdb-folder` option
(defaults to the current directory).
(d) An amino acid sequence corresponding to a CDR with 2 extra residues on
either side, e.g. `parapred cdr ARSGYYGDSDWYFDVGG`.
Multiple CDR sequences can be processed at once by specifying a file,
containing each sequence on a separate line (using the `--cdr-list` option).
Usage:
parapred seq <sequence>
parapred fasta <fasta_file>
parapred pdb <pdb_file> [--abh <ab_h_chain_id>] [--abl <ab_l_chain_id>]
parapred pdb --pdb-list <pdb_descr_file> [--pdb-folder=<path>]
parapred cdr <cdr_seq>
parapred cdr --cdr-list <cdr_file>
parapred (-h | --help)
Options:
-h --help Show this help.
seq Takes the full amino acid sequence of a VH or VL
domain (requires anarci).
fasta Takes a fasta-formatted file of amino acid
sequences corresponding or containing VH and VL
domains (requires anarci).
pdb PDB-annotating mode. Replaces B-factor entries
with binding probabilities (in percentages). PDBs
must be Chothia-numbered.
--abh <ab_h_chain_id> Antibody's heavy chain ID [default: H].
--abl <ab_l_chain_id> Antibody's light chain ID [default: L].
--pdb-list <pdb_descr_file> List containing PDB file names and chain IDs in CSV format.
--pdb-folder <path> Path to a folder with PDB files [default: .].
cdr <cdr_seq> Given an individual CDR sequence with 2 extra residues
on either side, outputs binding probabilities for each residue.
--cdr-list <cdr_file> List containing CDR amino acid sequences, one per line.➜ ~ parapred cdr ASGYTFTSYWI
... omitted TensorFlow messages ...
# ParaPred annotation of ASGYTFTSYWI
A 0.005611494
S 0.022217814
G 0.13472338
Y 0.3498
T 0.4621269
F 0.077797584
T 0.7191864
S 0.9059194
Y 0.8069638
W 0.9702157
I 0.014193774
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