Ali Saglam
Computational Chemist
Pittsburgh, Pennsylvania, United States
Summary
👤
Senior🎓
Top SchoolAli Saglam is a computational chemist and scientific programmer with a PhD and 13 years of experience translating advanced simulation methods into production-ready tools for drug discovery. He combines deep expertise in molecular dynamics, enhanced sampling (weighted ensemble), and high-performance computing with hands-on software engineering—shipping Metaflow and DVC pipelines, GPU-accelerated 3D similarity search tools, and automated workflows that power virtual screening and ABFE-driven SAR. At VantAI he led projects that integrated AI-generated protein-ligand refinement, automated ternary-complex ingestion, and PROTAC optimization (including a ~50-fold potency improvement), while earlier academia work produced widely used open-source tools like a BioNetGen Python front-end, a VS Code extension, and WEBNG for WESTPA integration. Comfortable across C/C++, Python, JavaScript and cloud/Kubernetes environments, he bridges research and industry by turning complex simulations into scalable, reproducible pipelines. He’s also an active maintainer and contributor to community science software, with released packages on PyPI and publications linked on Google Scholar.
13 years of coding experience
6 years of employment as a software developer
Doctor of Philosophy Chemistry, Doctor of Philosophy Chemistry at University of PittsburghBachelor of Science Chemistry, Bachelor of Science Chemistry at Marmara University
Github Skills (29)
simulation10
parallelization10
molecular-simulation10
computational-chemistry10
rule-based10
blender10
rule10
modeling10
molecule9
python9
rbm9
reaction-network9
cli8
weighted8
simplify8
Programming languages (6)
Github contributions (5)
westpa/westpa
Oct 2012 - Aug 2021
WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis
Contributions:382 commits, 33 PRs, 14 pushes in 8 years 11 months
parallelizationsimulationcomputational-chemistrymolecular-simulation
ASinanSaglam/BNGSim
Mar 2019 - Apr 2021
Contributions:111 pushes, 5 branches in 2 years 1 month
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