pocket_definition

Pocket-Definition

This scripts determine the KLIFS binding pocket numbering of the given Kinase.

Required Software:

• Clustal Omega
• EMBOSS
• BLAST+

Note: The following installation guide for Mac requires the package manager Homebrew. You can install Homebrew using:

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

Clustal Omega installation:

Linux

sudo apt install clustalo

Mac

# install argtable first
brew install argtable

# download clustal omega source code and unpack it
wget -qO- http://www.clustal.org/omega/clustal-omega-1.2.1.tar.gz > clustal-omega-1.2.1.tar.gz
tar zxvf clustal-omega-1.2.1.tar.gz

# install Clustal Omega
cd clustal-omega-1.2.1
./configure CFLAGS='-I/opt/homebrew/include' LDFLAGS='-L/opt/homebrew/lib'
make
make install

EMBOSS

Linux

sudo apt-get install emboss

Mac

brew install brewsci/bio/emboss

Blast+

Linux

sudo apt-get install ncbi-blast+

Mac

brew install blast

Usage

python3 pocket_definition.py [-h] -f FAMILY -n NAME -p PATH_TO_PDB_FILE

FAMILY should be replaced by the kinase's family (e.g., PKA), and NAME by the kinase's name (e.g., Prkaca).