Stephanie A. Wankowicz

Scientific Program Director, Prism
Assistant Adjunct Professor, Vanderbilt University

I am a computational structural biologist developing algorithms to model protein conformational ensembles from X-ray crystallography and cryo-EM data. My work reveals how protein dynamics and entropy govern biological function, specificity, and drug binding.

I lead the Prism Initiative at the Astera Institute. Our goal is to transform the field of structural biology to make protein motion measurable, predictable, and actionable.

Prism Publications CV
Stephanie A. Wankowicz

Latest Research

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WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures

2026

WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures

Srivastava V, Mai H, Collins M, Holton J, Wall M, Wankowicz SA. bioRxiv. 2026.

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Recovering Conformational Heterogeneity from the Protein Data Bank at Scale

2026

Recovering Conformational Heterogeneity from the Protein Data Bank at Scale

Wankowicz SA. The Stacks. 2026.

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2026

Supplying a user-defined bulk solvent map for refinement

Holton J, Wankowicz SA. The Stacks. 2026.

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sampleworks: A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation

2026

sampleworks: A Modular Platform for Experimentally Guided Biomolecular Ensemble Generation

Chrispens K, Collins MD, Mai D, Wankowicz SA, Fraser JS, van den Bedem H. The Stacks. 2026.

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Binding Entropy Can Be Predicted by Crystallographic Ensembles

2026

Binding Entropy Can Be Predicted by Crystallographic Ensembles

Miller CA, Wankowicz SA. bioRxiv. 2026.

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Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain

2025

Crystallographic Ensembles Reveal the Structural Basis of Binding Entropy in SARS-CoV2 Macrodomain

Seo L, Farran I, Aslam A, Li X, Jaishankar P, Ashworth A, Fraser JS, Renslo AR, Wankowicz SA....

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10 Rules for a Structural Bioinformatic Analysis

2025

10 Rules for a Structural Bioinformatic Analysis

Wankowicz SA. PLoS Computational Biology. 2025.

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Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments

2025

Expanding Automated Multiconformer Ligand Modeling to Macrocycles and Fragments

Flowers J, Echols N, Correy G, Jaishankar P, Togo T, Renslo AR, van den Bedem H, Fraser JS,...

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Research Interests

Using computational methods to understand how protein motion shapes function, with the goal of transforming structural biology and drug design.

🔬

Conformational Ensemble Modeling

Developing automated tools (qFit) to extract low-populated but biologically important protein states from X-ray crystallography and cryo-EM data.

⚡

Protein Dynamics & Entropy

Investigating how conformational entropy is spatially redistributed during ligand binding and catalysis, linking dynamics to thermodynamics.

🧬

Macromolecular Specificity

Exploring how protein and water dynamics interplay to shape substrate recognition, with implications for enzymatic specificity and drug selectivity.

💊

Ligand & Protein Engineering

Applying ensemble-based insights to revolutionize targeted ligand and protein design by accounting for the full thermodynamic landscape.

🤖

AI in Structural Biology

Integrating machine learning with structural bioinformatics to uncover patterns in protein dynamics at scale across the Protein Data Bank.

📂

Open Science & Reproducibility

Advocating for open-source software, transparent data sharing, and reproducible methods in structural biology and AI-driven research.

Podcast

The Tortured Proteins Department

A podcast co-hosted with James Fraser covering the latest in structural biology, protein dynamics, scientific policy, and life in academia.

Apple Podcasts Spotify

Episodes

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Episode 17

State of Decay

August 30, 2026

The seventeenth episode of The Tortured Proteins Department is out now! We discuss travels, awards, federal funding, preprints, and AI workflows for science. Apple Podcasts Spotify

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Episode 16

Cruel Kinase Summer

July 19, 2026

The sixteenth episode of The Tortured Proteins Department is out now! We discuss consortium meetings, OMB rules, miniprotein kinase preprints, and differences in scholarly work. Apple Podcasts Spotify

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Episode 15

Daylight

June 13, 2026

The fifteenth episode of The Tortured Proteins Department is out now! We discuss a conformational ensembles conference, NIH policy changes, four preprints, and running. Apple Podcasts Spotify

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Episode 14

Mastermind

May 8, 2026

The fourteenth episode of The Tortured Proteins Department is out now! We discuss NIH strategic planning, cryo-EM vitrification effects, agentic workflows, and AI lab guidelines. Apple Podcasts Spotify

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Episode 13

Long Live

April 6, 2026

The thirteenth episode of The Tortured Proteins Department is out now! We discuss NIH funding reports, grant termination demographics, protein design, and AI as graduate students. Apple Podcasts Spotify

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Episode 12

Science-ing Through the Lightning Strikes

February 22, 2026

The twelfth episode of The Tortured Proteins Department is out now! We discuss the Olympics, NIH bureaucracy, preprints on protein regulation and NMR exploration. Apple Podcasts Spotify

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Episode 11

Back to December

January 24, 2026

The eleventh episode of The Tortured Proteins Department is out now! We chat about travels, new preprints, and vibe coding. Preprints discussed in this episode: Improving Cryo-EM Optimization Robustness with...

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Episode 10

Science Tree Farm

December 20, 2025

The tenth episode of The Tortured Proteins Department is out now! Topics covered: Year in review 2026 predictions Links discussed in this episode: How to Not Make a Scientific Journal...

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Episode 9

I Can Do It With a Broken Grant Cycle

November 24, 2025

The ninth episode of The Tortured Proteins Department is out now! Topics covered: Government shutdown/reopening Travels The impact of Jane Richardson New science funding structures and Arena BioWorks closing AI...

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Episode 8

Open Science in a Changing Academic World

October 23, 2025

The eighth episode of The Tortured Proteins Department is out now! Topics covered: Compact for Academic Excellence in Higher Education Government shutdown HHMI’s new open science policies Shrinking PhD pools...

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Episode 7

Preprint Notifications and the Point of Rotations

September 27, 2025

The seventh episode of The Tortured Proteins Department is out now! Latest news: H1B changes and chaos; who determines what gets into PubMed (Literature Selection Technical Review Committee). Preprints discussed...

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Episode 6

Open Science and the Future of Engagement

August 31, 2025

The sixth episode of The Tortured Proteins Department is out now! We chatted about recent meetings, latest news, open science, social media, and, of course, the recent engagement. Preprints and...

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Episode 5

NIH Ghosting, Open Access Policies, and Scientists' Interaction with LLMs

July 12, 2025

The fifth episode of The Tortured Proteins Department is out now! We chatted about the latest news, including the new NIH open access policy, trends observed with scientists using LLMs,...

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Episode 4

Conformational Ensembles & Teaching Vibe Coding

June 24, 2025

The fourth episode of The Tortured Proteins Department is out now! We chatted about the latest news, our Conformational Ensembles Conference, vibe coding in science, and the Dipsea and Montpelier...

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Episode 3

Travels, Protein Folding, Side Chain Dynamics, and Strava Kudos

May 16, 2025

The third episode of The Tortured Proteins Department is out now! We discussed grant cancellations, exciting regional meetings and reunions, two fun new preprints, community norms surrounding code release, and...

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Episode 2

Cool Science Among Continued Uncertainty

April 15, 2025

The second episode of The Tortured Proteins Department is out now! We chatted about the continued chaos of science infrastructure and dived into some cool science from recent meetings James...

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Episode 1

Scientific Uncertainty and Graduate Education

March 15, 2025

James Fraser and I have started a podcast called the Tortured Proteins Department. The first episode is out now! We discuss the declining support of science in the US and...

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Contact

I'm always happy to discuss research, collaborations, and opportunities.

Institution
Radial, Astera Institute

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