Graph-based Rigid Domains Estimator
Ubuntu 16.04 LTS or later
Python 3.7
biopython (1.78 or later) from https://biopython.org/
csb (1.2.5 or later) from https://csb.codeplex.com/
louvain (0.6.1) from https://pypi.python.org/pypi/louvain/
matplotlib (only to draw praph) (3.0.3 or later) from matplotlib.org
numpy (1.16.4 or later) from https://numpy.org/
python-igraph (0.7.1) from https://igraph.org/python/
scikit-learn (0.21.3 or later) from https://scikit-learn.org/stable/
scipy (1.3.1 or later) from https://www.scipy.org/
MDAnalysis (0.20.1 or later) from https://www.mdanalysis.org
cairocffi (1.1.0 or later)
clustal omega
(sudo apt-get install -y clustalo)
python3.7-dev
(sudo apt install python3.7-dev)
Clone project from https://github.com/dtklinh/GBRDE.git
(git clone https://github.com/dtklinh/GBRDE.git)
Go to GBRDE folder and run one of those command lines:
1. Run by a list of PDBID, for example
./venv/bin/python3.7 GBRDE.py -n 'adk' -t 'list' -i '1ake_A, 4ake_A' -a 7.5 -r 3.5 -g 1.0
2. run by a xyz file, for example
./venv/bin/python3.7 GBRDE.py -n 'lys' -t 'xyz' -i '.test/data/lysozyme.xyz' -a 7.5 -r 3.5 -g 1.0
3. Run by a pdb file, for example
./venv/bin/python3.7 GBRDE.py -n 'adk' -t 'pdb' -i './test/data/adk.pdb' -a 7.5 -r 3.5 -g 1.0
GBDE.py parameters:
-n <ProteinName> # any name
-t <TypeOfFile> # one in three {'list', 'pdb', 'xyz'}
-i <inputfile> # if TypeOfFile is 'pdb' or 'xyz', then it is a path to a file
if TypeOfFile is 'list', it is a list, e.g. '1ake_A, 4ake_A'
-a <AA_cutoff> # default: 7.5
-m <init_membership>, # default: None
-r <rigid_thres> # default: 3.5
-g <merging_thres> # default: 1.0
-o <output_directory>' # default: current working directory
http://azifi.tz.agrar.uni-goettingen.de/webservice/
There are three possible ways to upload a file and run the web-service
-
Run by a PDB file File format: PDB format where a protein structure contains only one chain (default chain A) with at least two models (conformations) of this chain. The file example could be found at the web-service
-
Run by a XYZ file File format: XYZ format. This file contains at least two models/conformations of a protein chain. The file example could be found at the web-service.
-
Run by a list of PDB IDs File format: a text file whose each line is a PDB code and a chain name of a protein chain, separated by an underscore. (For example: 1ake_A) The text file has to consist of at least two lines. The file example could be found at the web-service.