Alberto Perez

About

Alberto Perez is William R. Kenan, Jr. Term Associate Professor and Associate Director at the Quantum Theory Project within the Department of Chemistry at the University of Florida. His research focuses on developing and applying computational chemistry tools to understand how biomolecules work and their role in disease. Using a combination of AI and physics-based methods, he is building drug discovery pipelines that target peptides and DNA aptamers. Perez is also dedicated to scientific communication, engaging in VR and AI–driven projects to collaborate with high school students and help them experience research firsthand. His educational background includes a PhD in Computational and Theoretical Chemistry from the University of Barcelona, postdoctoral fellowships at USCF, Stony Brook University, IRBB, and Barcelona Supercomputer Center, and a B.S. in Chemistry from the University of Barcelona. He has received several awards, including the NSF CAREER Award in 2022, the ACS OpenEye Cadence Outstanding Junior Faculty Award in 2023, and the Japanese Society for the Promotion of Science Long Term Fellow in 2023. Perez actively participates in organizing scientific symposia and serves on editorial boards, contributing to the advancement of computational chemistry and biophysics.

Research topics

• Computer Science
• Computational biology
• Biology
• Data Mining
• Chemistry
• Biochemistry
• Data science
• Combinatorial chemistry
• Bioinformatics
• Physics

Selected publications

• Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

  Nature Methods · 2021 · 118 citations

  This paper describes outcomes of the 2019 Cryo-EM Model Challenge. The goals were to (1) assess the quality of models that can be produced from cryogenic electron microscopy (cryo-EM) maps using current modeling software, (2) evaluate reproducibility of modeling results from different software developers and users and (3) compare performance of current metrics used for model evaluation, particularly Fit-to-Map metrics, with focus on near-atomic resolution. Our findings demonstrate the relatively…

  DOI

• Ranking Peptide Binders by Affinity with AlphaFold**

  Angewandte Chemie International Edition · 2022 · 80 citations

  Senior authorCorresponding

  AlphaFold has revolutionized structural biology by predicting highly accurate structures of proteins and their complexes with peptides and other proteins. However, for protein-peptide systems, we are also interested in identifying the highest affinity binder among a set of candidate peptides. We present a novel competitive binding assay using AlphaFold to predict structures of the receptor in the presence of two peptides. For systems in which the individual structures of the peptides are well pr…

  DOI

• RNA-Puzzles Round V: blind predictions of 23 RNA structures

  Nature Methods · 2024-12-02 · 60 citations

  articleOpen access

  RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between predicti…

  PublisherOA PDFDOI

• The need to implement FAIR principles in biomolecular simulations

  Nature Methods · 2025-04-01 · 53 citations

  articleOpen access
  PublisherOA PDFDOI

• CryoFold: Determining protein structures and data-guided ensembles from cryo-EM density maps

  Matter · 2021 · 51 citations

  Cryo-electron microscopy (EM) requires molecular modeling to refine structural details from data. Ensemble models arrive at low free-energy molecular structures, but are computationally expensive and limited to resolving only small proteins that cannot be resolved by cryo-EM. Here, we introduce CryoFold - a pipeline of molecular dynamics simulations that determines ensembles of protein structures directly from sequence by integrating density data of varying sparsity at 3-5 Å resolution with coar…

  DOI

Recent grants

• CAREER: Enhanced Sampling Methods to Characterize Nucleic Acid Structure, Recognition Mechanisms and Function

  NSF · $650k · 2022–2027

Frequent coauthors

• Modesto Orozco

  Universitat de Barcelona

  249 shared

• Jiřı́ Šponer

  Czech Academy of Sciences, Institute of Biophysics

  82 shared

• Richard Lavery

  Institut de Biologie et de Chimie des Protéines

  80 shared

• Charles A. Laughton

  University of Nottingham

  62 shared

• Thomas E. Cheatham

  University of Utah

  57 shared

• Filip Lankaš

  University of Chemistry and Technology, Prague

  49 shared

• Ken A. Dill

  Stony Brook University

  48 shared

• K. Zakrzewska

  University of Florence

  48 shared

Education

• Ph.D., Physical Chemistry

  University of Barcelona

  2008

• Chemistry

  University Of Barcelona

  2002

Awards & honors

• Japanese Society for the Promotion of Science (JSPS) Long Te…
• ACS OpenEye Cadence Outstanding Junior Faculty Award / ACS C…
• NSF CAREER Award (2022)
• European Molecular Biology Organization (EMBO) postdoctoral…
• Juan de la Cierva Postdoctoral fellowship (2009)

Similar researchers at University of Florida

• George Christouh-133
• Rodney J. Bartletth-118
• Richardsonh-50