Yoonjoo Choi

PREpiBind: Protein Representation-integrated Epitope-MHC Class II Binding Prediction

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

Benchmarking Sequence-Based and AlphaFold-Based Methods for pMHC-II Binding Core Prediction: Distinct Strengths and Consensus Approaches

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.

AI-Informed neoantigen prioritization enables a multi-epitope mRNA/LNP vaccine with antigen-specific immunogenicity and antitumor activity

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

Changes in biophysical characteristics of YghA from E. coli due to variation in pH

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.

Structure-guided deimmunisation of Fel d 1 suppresses allergic effector functions ex vivo

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: Structure-based machine learning approach to pMHC-I binding prediction using force field energy features

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.

Allosteric deimmunisation of a Salmonella phosphatase enhances catalytic function

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

Assessing the Predictive Ability of Computational Epitope Prediction Methods on Fel d 1 Allergen and Other Allergens

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.

Fever temperatures modulate intraprotein dynamics and enhance the binding affinity between monoclonal antibodies and the Spike protein from SARS-CoV-2

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

Computer-guided Binding Mode Identification and Affinity Improvement of an LRR Protein Binder without Structure Determination

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: Computational Algorithm for the Design of Complementary β-sheet Sequences

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