Cross Platform commandline software to Automate the time consuming process before docking

The project automates the process of extracting protein targets for a given Pubchem CID. It performs the following steps:

• Generate conformations of the given Pubchem CID using Balloon
• Scrapes SwissTargetPrediction for gene names related to the Pubchem CID
• Get protein-protein interaction network by scraping String DB
• Extracting Top 3 genes from this network by use of Kmeans Clustering
• Retrieve PDB files corresponding to these genes
• Purifying thee PDB files (Removing water molecules, Hetero Atoms, Chains {User selected})
• Move generated files to a timestamped folder.

• REQUIRES CHROME TO RUN!!!
• Install requirements

pip install -r requirements.tst

• Run the python file main.py.
• Software will prompt you accordingly

• main.py
  • Core file that brings it all together
• balloon_run.py
  • Runs conformational search on the given Pubchem CID and gives a total of 20 conformations using Balloon software
  • MMFF94.mff forcefield file and balloon.exe is included (balloon for linux support)
• swiss_target_scrapper.py
  • Scrapes SwissTargetPrediction
• gene_names.py
  • Extracts gene names obtained into a separate txt file
• string_db_scrapper.py
  • Scrapes Strind-DB
• g2p_puri.py
  • Retrieves PDB structures and purifies them

• Pandas
• Selenium
• Biopython
• Pubchempy
• Balloon

This project is licensed under the MIT License.