Yoonjoo Choi

PREpiBind evaluates ten protein representations for pMHC-II binding prediction across multiple datasets, showing varying performance depending on the task and evaluation method.

This paper benchmarks sequence-based and AlphaFold-based methods for predicting pMHC-II binding cores, finding that AlphaFold-based methods excel at identifying binders while NetMHCIIpan is better at identifying non-binders.

This paper develops a multi-epitope mRNA/LNP vaccine using AI-prioritized neoantigens, showing enhanced immunogenicity and antitumor activity in preclinical models.

This study examines how pH changes affect the biophysical properties of YghA from E. coli, revealing structural instability at acidic pH and altered interactions with NADH.

This study designs hypoallergenic variants of Fel d 1 by disrupting IgE-binding sites, showing reduced IgE reactivity and suppressed basophil activation ex vivo.

STRUMP-I improves pMHC-I binding prediction by using force-field energy features, outperforming sequence-based methods on underrepresented MHC alleles and showing synergy with them.

This study deimmunizes a Salmonella phosphatase by mutating buried residues, enhancing its catalytic function while reducing immunogenicity.

This study evaluates computational epitope prediction tools on Fel d 1 allergen and other allergens, finding limited effectiveness and highlighting the need for improved methods.

The paper identifies cancer-specific transposon-fusion RNAs across 34 cancer types and finds they are associated with tumor suppressors and oncogenes, and can activate T-cells.

The paper investigates how mild fever temperatures affect the binding affinity of antibodies to the SARS-CoV-2 Spike protein using molecular dynamics simulations.

The paper develops a method combining computational and experimental approaches to identify binding modes and improve affinity of an LRR protein binder without structure determination.

B-SIDER is a computational method for designing complementary β-strands that outperforms existing methods in distinguishing amyloidogenic β-strands.