Description

Part of RESMATCH program at Illinois Tech, I got opportunity to work under Prof. Andew Howard as student researcher in Fall 2024. I worked on the project of Analysis and Replacement of water molecules in the crystals

My roles and responsibilities

  • The project focuses on leveraging computational tools for analyzing water interactions within protein structures. Initially, I explored protein structures and data available in the Protein Data Bank (PDB) while familiarizing myself with the CloseWat software for preliminary analysis. Transitioning to hands-on computational work, I began developing Python scripts to extract and analyze water-specific details but shifted the focus to rebuilding and manipulating protein structures. Utilizing tools like Phenix and Coot, I gained proficiency in structural refinement, including interpreting PDB data formats and manipulating three-dimensional electron density maps. Throughout the research I did the full cycle of refinement of a Green Fluorescent Protein (6JGI) and performed the manipulation and validation of protein structures in Coot.

Methods and Tools:

  • We used the Phenix (Python-based Hierarchical Environment for Integrated Xtallography) for automated structure refinement utilizing the phenix.refine method
  • We used BLASTP for sequence comparison among that of Source and Target.
  • We used Coot for redetermining the water position and did the validation of structure using various functions for different part of validation. I also did the manual adjustment of protein structure to fit the expected structure.

Tech Stack

  • Python
  • Coot
  • Phenix
  • BLASTP
  • PDB (Protein Data Bank)

Responsibilities

  • Attended weekly meetings with Professor to discuss about the progress and challenges.
  • Helped the students of BME 555 in installing the and configuring the softwares like coot and phenix.
  • Got familiar with the lab work done by biomedical students in finding the experimental results and comparing against the computational results.
  • Actively worked on the different output format, data preprocessing, extracting the required data from Protein Data Bank and finally redermining the position of HOH molecules in the protein structure.
  • Experimented with different output formats like FASTA sequence, CIF format, PDB format. I also worked with Data API proviced by RCSB PDB site, to efficiently work with the data.