LOKESH BAWEJA
Chicago,USA
Summary
Accomplished Computational Chemist with a proven track record at the Illinois Institute of Technology, adept in molecular simulations and fostering collaborations. Spearheaded groundbreaking research, leading to multiple high-impact publications and a $50,000 grant. Expert in Python and influential in team settings, seamlessly integrating computational models with experimental data to advance drug discovery.
Overview
9
9
years of professional experience
Work History
Computational Chemist
Illinois Institute of Technology
Chicago, IL
09.2018 - Current
- Investigated epigenetics drug targets and DNA dynamics through various computational chemistry methods
- Constructed quantitative structure activity relationship (QSAR) models for identifying small molecules properties responsible for RNA binding
- Designed computational data modeling to explain the peptide binding interactions observed in ITC experimental assays, leading to a first author publication in Journal of Chemical Information and Modeling
- Implemented docking and free-energy perturbation (FEP) calculations to evaluate the isoform selectivity of small molecules for chromatin readers
- Developed workflows with Python and shell scripting for processing and analyzing large scale simulation data to communicate scientific findings in 4 publications
- Collaborated with experimentalists to interpret NMR data on protein-oligonucleotide systems, resulting in a publication in Nucleic Acids Research
- Integrated computer simulations and free-energy analysis to predict targeted protein degraders affinities
- Benchmarked molecular dynamics packages on HPC platforms for computational grants with principal investigator securing funding of $50,000
Postdoctoral Associate
Iowa State University
Ames, IA
02.2017 - 08.2018
- Structure-based design and method optimization for protein folding and protein-protein associations
- Parameterize the structure based force-field to simulate the folding of repeat proteins and the protein-protein associations, resulting in a computationally efficient alternative to explicit molecular dynamics (MD)
- Integrated structure-based models with physics-based enhanced sampling protocol to identify novel intermediates along the transthyretin oligomerization pathway
Research Fellow
Indian Institute of Technology
Gujarat, India
04.2016 - 02.2017
- Developed in silico models of Tau fibrils for screening of anti-amyloid small molecules
- Collaborated with a graduate student to generate computational models of tau peptide fibrils for screening 2 age-related post-translational modifications
- Generated a simulation based model to screen small molecules for their anti-amyloid properties
Education
PhD - Computational Biophysics
Academy of Scientific and Innovative Research
12.2015
Master of Science - Biotechnology
MS University of Vadodara
07.2009
Bachelor of Science - Chemistry and Biotechnology
Rohilkhand University
08.2007
Skills
- Molecular simulations
- AMBER
- GROMACS
- NAMD
- Schrödinger
- Docking workflows
- Virtual screening workflows
- RDKit
- Open Babel
- Jupyter notebook
- Free-energy perturbation (FEP)
- Lead optimization
- Machine learning models
- Numpy
- Scikit-learn
- PyTorch
- Python
- Linux scripting
- Fortran
- Sequencing data analysis
- Therapeutic target identification
- Biological systems simulations
- PROTACs
- DNA
- Proteins
- Communication
- Influencing skills
Researchpublications
- Baweja, L., Wereszczynski, J., Conformational and Thermodynamic Differences Underlying WildType and Mutant Eleven Nineteen Leukemia YEATS Domain Specificity for Epigenetic Marks., Journal of Chemical Information and Modeling, 02/01/23
- Clayton, J., Baweja, L., Wereszczynski, J., Peptide Dynamics and Metadynamics: Leveraging Enhanced Sampling Molecular Dynamics to Robustly Model Long-Timescale Transitions., Computational Peptide Science Methods and Protocols, 12/01/22
Leadership Experience
- Led a team of scientists to secure a funding of $50,000.
- Organized and conducted Python programming boot camps, equipping four new team members with essential computational skills.
Timeline
Computational Chemist
Illinois Institute of Technology
09.2018 - Current
Postdoctoral Associate
Iowa State University
02.2017 - 08.2018
Research Fellow
Indian Institute of Technology
04.2016 - 02.2017
PhD - Computational Biophysics
Academy of Scientific and Innovative Research
Master of Science - Biotechnology
MS University of Vadodara
Bachelor of Science - Chemistry and Biotechnology
Rohilkhand University
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