Loading PDBBIND.md 0 → 100644 +22 −0 Original line number Diff line number Diff line # Setting up PDBBind example First, ensure that you are in the correct environment, and then download the pdbbind reference database: ```bash source activate deepchem (deepchem) user@server:~/deepchem/examples/pdbbind$ ./get_pdbbind.sh ``` You will see a large number of directories created with PDB (protein) and SDF (ligand) files, for instance: ```bash v2015/3d1g/3d1g_ligand.mol2 v2015/3d1g/3d1g_pocket.pdb v2015/3d1g/3d1g_protein.pdb v2015/3d1g/3d1g_ligand.sdf ``` Next, you can train the Random Forest-based classifier via: ```bash (deepchem) ubuntu@ip-172-31-12-186:~/deepchem/examples/pdbbind$ python pdbbind_rf.py ``` TODO: Add notes about how to expand the v2015 dataset, e.g. to add protein 14HR as associated with NF2 to the analysis Loading
PDBBIND.md 0 → 100644 +22 −0 Original line number Diff line number Diff line # Setting up PDBBind example First, ensure that you are in the correct environment, and then download the pdbbind reference database: ```bash source activate deepchem (deepchem) user@server:~/deepchem/examples/pdbbind$ ./get_pdbbind.sh ``` You will see a large number of directories created with PDB (protein) and SDF (ligand) files, for instance: ```bash v2015/3d1g/3d1g_ligand.mol2 v2015/3d1g/3d1g_pocket.pdb v2015/3d1g/3d1g_protein.pdb v2015/3d1g/3d1g_ligand.sdf ``` Next, you can train the Random Forest-based classifier via: ```bash (deepchem) ubuntu@ip-172-31-12-186:~/deepchem/examples/pdbbind$ python pdbbind_rf.py ``` TODO: Add notes about how to expand the v2015 dataset, e.g. to add protein 14HR as associated with NF2 to the analysis
