Experience
Research Experience
MAIL LAB, Carnegie Mellon University
Research Assistant Aug 2022 - Present
Project1/Master’s Thesis: Predicting Interactions in Heterodimeric Complexes using Multimodal Data Integration: Integrating GeomEtry-Aware Relational Graph Neural Network (GearNet)and Language Models in a Supervised Framework, with Self-supervised Insights.
The project aims to advance the understanding of protein/subunit interactions within heterodimeric complexes by leveraging multimodal data integration and state-of-the-art machine learning techniques. By predicting interactions between protein residues, the project seeks to understand the underlying biological mechanisms governing complex formation, which could have significant implications for drug discovery and therapeutic interventions. Co-author paper currently in preparation for submission to NeurIPS 2024. Report
Project 2: Peptide Property prediction of short-length peptides using GNNs and PeptideBERT. The purpose of the project was to develop and fine-tune PeptideBERT, a state-of-the-art protein language model based on Transformers,specifically designed for predicting important properties of peptides. PeptideBERT was trained using ProtBERT, a pre-trained transformer model specialized for protein sequences. Published a paper.
Project 3: The purpose of the second part of the project is to develop a robust framework for predicting properties of short-length peptides by leveraging advanced techniques from graph neural networks (GNNs) and protein language models. Specifically, the project utilizes the fine-tuned PeptideBERT and a Geometry-Aware Relational Graph Neural Network as encoders to capture both sequence and structural information of peptides.
Generative AI Innovation Incubator, Carnegie Mellon University
Aug 2023- Present
Application of encoder-only models for the design of inhibitor sequences, followed by their optimization through Adaptive Exploration in Multi-Objective Thompson Sampling-Guided Directed Evolution.
Description: Implementing Thompson Sampling-guided Directed Evolution (TS-DE) framework for multi-objective protein sequence optimization, integrating adaptive exploration techniques to balance and optimize conflicting objectives simultaneously. Additionally, incorporated tree-based neural bandits to further optimize exploration strategies and accelerate the discovery of high-performing protein sequences.
MAIL LAB, Carnegie Mellon University
Graduate Student Researcher
August 2022 - April 2023
- Applied various shallow machine learning models to understand the dynamics of trans-membrane proteins such as GPCRS. Performed the MD simulation of GPCRs using OpenMM and VMD and RL and automated it with the machine learning model.
Molecular Chemistry Lab, Vellore Institute of Technology
Undergraduate Student Researcher
November 2018 – August 2022
- Performed mass spectrometric analysis of the actions of AspN,LysC and GluC on some therapeutic antibodies to determine the length(size) distribution of polypeptides that result from the proteolysis of those antibodies.Used DeepPep as a tool for the analysis of MS-MS data.
- Worked on molecular docking analysis of natural products for the inhibition of the main protease of SARS-Cov-2 and repurposing drugs against the main protease of SARS-CoV-2.
- Worked on investigating the solvatochromic(fluorescence) properties of Bromophenol Blue in organic solvents in order to probe protein folding or protein binding studies in organic solvents. Performed UV-Vis spectroscopic, mass-spectrometric , FTIR and NMR spectroscopic analysis for carrying out this investigation.
- Presented findings at the International Conference of Chemical Sciences and Nanomaterials(2019) and at 26th CRSI National Symposium on Chemistry- Royal Society of Chemistry (2020).
Cellular Biomechanics Lab, Vellore Institute of Technology
Undergraduate Project Assistant
June 2019 – October 2019
- Performed design,characterization and in vitro evaluation of thin films enriched by tannic acid complexed by Fe(III) ions for potential applications as wound dressing.
- Employed techniques such as FTIR spectroscopy,SEM and UV-Vis spectroscopy for characterization of the films.
- Different tests and measurements were being performed for the films including contact angle measurements, blood compatibility tests,platelet adhesion tests and MTS Assay. The results of the MTS assay were being analyzed one-way ANOVA. Published a paper.
Molecular Biophysics Unit, Indian Institute of Science
Undergraduate Summer Research Assistant
June 2019 – October 2019
- As an undergraduate researcher, I embarked on a fascinating project on investigating the reaction of phenylglyoxal and arginine residues with proteins.
- Employed the powerful tool of NMR spectroscopy, specifically using C13 and H1 NMR techniques
- Conducted experiments in varying pH levels and concentrations and examined how these factors influenced the reaction outcome.
- Expanded my knowledge of advanced NMR techniques such as TOCS, COSY and NOESY.Delved into NMR pulse programming which involved designing and implementing precise sequences of radiofrequency pulses to optimize data acquisition and extract maximum information from the samples.
Please do reach out to me through email, if you have any questions about my research. I’d love to talk more!