Fine-Tuning DiffDock-L for Allosteric Kinase Docking
Chen, E. A., Greene, J. & Zhang, Y. (2025). "Fine-Tuning DiffDock-L for Allosteric Kinase Docking"
CV
Education
- Ph.D in Chemistry, New York University, Sep 2019–Aug 2025
- B.S. in Biochemistry, Tufts University, Sep 2015–May 2019
Select work experience
- Jan 2020–Aug 2025: New York University–Dept. of Chemistry: Graduate Research Assistant
- Perform model fine-tuning and benchmarking on a curated database and increase the success rate of molecular generative models to predict allosteric ligand poses to the kinome by 34%
- Establish data-driven, ML workflow and toolkit to analyze protein–ligand conformational heterogeneity and assess prospective docking applications of allosteric compounds
- Collaborate across cross-functional teams with experimentalist to determine the binding location of a hit and with a software engineer to design robust training procedures and strategies
- Perform ensemble docking, molecular dynamics and free energy calculations to guide experimental direction of binding site determination of hit compound
- Developed reproducible code and workflows with documentation and tutorials, using best practices with Git, testing, and containerization on an HPC cluster
- Supervisor: Yingkai Zhang
- Aug 2017–May 2019: Tufts University–Dept. of Chemistry; Undergraduate Research Assistant
- Utilize Bias-Exchange metadynamics for enhanced sampling of peptide macrocycles conformations
- De novo structure-based drug design of peptide macrocycle–collagen interactions by characterizing structural ensembles
- Supervisor: Yu-Shan Lin
Publications
Can Deep Learning Blind Docking Methods be used to Predict Allosteric Compounds?
Chen, E. A., & Zhang, Y. (2025). "Can Deep Learning Blind Docking Methods be used to Predict Allosteric Compounds?" J. Chem. Inf. Model. 65(7), 3737–3748.
A repurposed drug interferes with nucleic acid to inhibit the dual activities of coronavirus Nsp13
Soper, N.*, Yardumian, I.*, Chen, E. A.*, Yang, C., Ciervo, S., Oom, A., Desvignes, L., Zhang, Y., & Lupoli, T. (2024). "A repurposed drug interferes with nucleic acid to inhibit the dual activities of coronavirus Nsp13." ACS Chem. Biol. 19(7), 1593-1603.
Integrated Molecular Modeling and Machine Learning for Drug Design
Xia, S.*, Chen, E. A.* & Zhang, Y. (2023). "Integrated Molecular Modeling and Machine Learning for Drug Design." J. Chem. Theory Comput. 19, 7478–7495.
Protein–Ligand Docking in the Machine-Learning Era
Yang, C., Chen, E. A. & Zhang, Y. (2022). "Protein–Ligand Docking in the Machine-Learning Era." Molecules 27, 4568.
Using synthetic peptides and recombinant collagen to understand DDR–collagen interactions
Chen, E. A. & Lin, Y.-S. (2019). "Using synthetic peptides and recombinant collagen to understand DDR–collagen interactions." Biochim. Biophys. Acta - Mol. Cell Res. 1866, 118458.
Talks/Conferences/Posters
Tuning diffusion docking models for allosteric structure-based drug design to the kinome
Poster at AI4Chemistry-New York, NY; Gordon Research Conference-Portland, ME; MLDD Broad Institute Symposium-Cambridge, MA,
Teaching
DEI & Outreach/Leadership
- Aug 2025–Present: Gotham Data Clinic: Volunteer Program Assistant
- Assist development of a new non-profit through programming and event planning
- Sep 2021–May 2025: NYU–Chemistry; DEI/Outreach Working Group Co-chair
- Develop and execute the first strategic plan over 3 years to expand outreach efforts to enhance community engagement and diversity initiatives.
- Initiate and serve as the primary liaison for underserved NYC high school
- Lead group of 10–15 graduate students, faculty, and administrators to design chemistry outreach programming, oversee budget and impact assessment
- Organize and manage an annually run program that brings together up to 40 students and 80 volunteers for hands-on chemistry demonstrations, lunch, and building tours
- Recipient of the 2025 DEI/Outreach Student Organizer Award
- Sep 2021–May 2023: FOCUS Mentorship Program; Volunteer Mentor
- Mentor first-year, first-generation POC undergraduates to facilitate college transition by building confidence, introducing resources, and encouraging community and academic success.
- Jun 2019–Aug 2019: Gardner Pilot Academy Community School; Middle School Enrichment Teacher
- Create and lead daily science, cultural, arts and sports programming aligned with Massachusetts state standards for summer school students
- Support staff to create positive environment for student development
- Tufts Ultimate Frisbee Team; Sep 2017–May 2019: Captain: A Team: Sep 2015–May 2019
- Logistical, organizational, strategic and financial responsibilities of a nationally competitive team and coaching staff
- 2019 Callahan Nominee