Python For Cheminformatics-Driven Molecular Docking
Webinar hosted by RCSB PDB, Rutgers Artificial Intelligence and Data Science (RAD) Collaboratory, Rutgers Institute for Quantitative Biomedicine, and MolSSI | May 1, 2024
This workshop uses Python scripting to explore and compare small molecules that bind to the SARS-CoV2 main protease. Work is performed in a Google CoLab environment and involves a number of libraries heavily used for cheminformatics.
Course Objectives and Intended Audiences
After watching the videos in this course, you will be able to:
- Search BindingDB and create molecular datasets
- Use RDKit to manipulate and process molecules
- Compare features of families of small molecules using plots and fingerprint analysis
- Create a workflow for docking multiple ligands to the main protease (using gnina)
This course is intended for:
- Undergraduate students in any STEM discipline
- Graduate students and postdoctoral researchers in life sciences and data collection
- Faculty members who want to incorporate Python scripting into their teaching or research
- Professionals involved in collecting and analyzing data, particularly big data
Additional Resources
Preparation Guides for New Students
|
Video Guide |
Corresponding Google CoLab Notebook |
Notebook with Answers |
|---|---|---|
Course Videos
Click on the image below to play the video.
Introduction
Paul A. Craig
Professor of Biochemistry, Rochester Institute of Technology (RIT)
Exploring Chemical and Biological Data With BidingDB and the RDKit
Pat Walters
Chief Data Officer, Relay Therapeutics
Preparing Molecules and Proteins for Docking
Levi Naden
Software Scientist, Molecular Sciences Software Institute (MolSSI)
A Molecular Docking Workflow
Jessica Nash
Software Scientist, Molecular Sciences Software Institute (MolSSI)
