Shubham Pandey

I work at the intersection of machine learning, molecular modeling, and computational biology to explore protein function, drug discovery, and the molecular basis of life.
With a multidisciplinary background in pharmacoinformatics, chemical engineering, and AI, I build predictive models, run molecular dynamics simulations, and analyze complex biological systems using high-performance computing.
Whether it's simulating protein behavior or screening millions of compounds, I am passionate about using computation to solve real-world biological problems.

Things I Can Do

I like solving science problems with code. Whether it's simulating molecules, building machine learning models, or spinning up a quick web app — here's what I bring to the table, line by line.

• vi ~/.bashrc
• Build machine learning models to decode biological patterns
• Simulate proteins and reveal their dynamic behavior over time
• Run late-night docking jobs
• Find patterns in chemical structures
• Read papers, break them down, and turn ideas into code
• Teach workshops, mentor peers, and build a data-savvy crew

My learning story

A Few Accomplishments

Some highlights from my academic, research, and teaching journey so far — from running simulations and publishing papers to mentoring students and leading workshops.

Selected for Statewide 3MT Competition
University of Idaho

Competed in the Three-Minute Thesis (3MT) competition at the college level and was selected to represent the University of Idaho at the statewide 3MT showcase, which will be held in Coeur d’Alene.

Presented at the MDAnalysis User Group Meeting 2025
Arizona State University, Tempe, AZ

Delivered a lightning talk showcasing my PhD research, integrating AI and molecular modeling with MDAnalysis to study color tuning in microbial rhodopsins.
Received a Travel Award to attend the meeting.

Institute for Modeling Collaboration and Innovation (IMCI)
University of Idaho

Appointed as Data Carpentries Teaching Assistant (Spring 2026) with IMCI, supporting genomics and machine learning workshops.

Presented at ACS Spring 2025
San Diego, CA

Title: Unraveling Spectral Shifts in Microbial Rhodopsins through Machine Learning and Molecular Dynamics
Showcasing the integration of machine learning models and molecular dynamics simulations to predict and interpret spectral shifts in rhodopsin proteins.

Featured by University of Idaho
College of Engineering

For NIH-supported research using AI and molecular modeling to address color blindness through opsin protein mutation analysis.

Awarded the Outstanding Teaching Assistant Award
University of Alabama, Tuscaloosa, AL

For exceptional instructional support and student mentorship in computational and lab-based courses.

Recipient of the Chancellor’s Scholarship, conferred by the Governor of Madhya Pradesh.

Awarded the Chancellor’s Scholarship in recognition of being a top scorer across 98 affiliated pharmacy colleges under RGPV, Bhopal.

Contact Me

Interested in computational biology, machine learning, or molecular simulations?
Reach out 🙋🏻‍♂️ I am always open to research conversations and potential collaborations.