Alberto Perez
William R. Kenan, Jr. Term Associate Professor & Associate Director Quantum Theory Project
Research Focus
We develop and apply computational chemistry tools to understand how biomolecules work and their role in disease. Using a combination of AI and physics-based methods, we are building drug discovery pipelines focused on peptides and DNA aptamers. In teaching, we cover a broad range of topics—from computational chemistry and statistical mechanics at the graduate level to general chemistry honors and physical chemistry for biosciences at the undergraduate level. We are also passionate about scientific communication. Through VR and AI–driven projects, we collaborate with high school students to let them experience the excitement of research firsthand. If you share our interest in science communication and want to help expand these efforts, we’d love to hear from you!
Education and Training
2010–2018. EMBO Postdoc/Junior Fellow at USCF and Stony Brook University (lab of Ken Dill)
2008–2010: Postdoc IRBB and Barcelona Supercompter Center (labs of Modesto Orozco and David Torrents)
2003–2008: PhD Computational and Theoretical Chemistry, University of Barcelona (labs of Modesto Orozco and F. Javier Luque)
1998–2002: B.S Chemistry, University of Barcelona
Selected Awards
Japanese Society for the Promotion of Science (JSPS) Long Term Fellow (2023)
ACS OpenEye Cadence Outstanding Junior Faculty Award / ACS Computational (2023)
Chemistry NSF CAREER Award (2022)
European Molecular Biology Organization (EMBO) postdoctoral Fellowship (2010)
Juan de la Cierva Postdoctoral fellowship (2009)
Selected Activities
Organizing committee Sanibel Symposium (Quantum Theory Project) (2021–)
Organizer Biophysical Society Thematic meeting In Hamburg (2022): Biophysics at the dawn of exascale computers
Organizing committee MSAM Workshop (Kobe, Japan, May 2026)
Standing member NIH/NIGMS MSFA (2025–)
Current Computer-Aided Drug Design Editorial Board (2019–)
Selected Publications
Silva, N. D.; Perez, A.* Predicting Rare DNA Conformations via Dynamical Graphical Models: A Case Study of the B→A Transition. Nucleic Acids Res. 2025, 53, gkaf601.
Mondal, A.; Singh, B.; Felkner, R.; De Falco, A.; Swapna, G. V. T.; Montelione, G.; Roth, M.; Perez, A.* A Computational Pipeline for Accurate Prioritization of Protein–Protein Binding Candidates in High-Throughput Protein Libraries. Angew. Chem. Int. Ed. 2024, 63, e202405767.
Chang, L.; Perez, A.* Ranking Peptide Binders by Affinity with AlphaFold. Angew. Chem. Int. Ed. 2023, 62, e202213362.