Leveraging Large Language Models to Predict Antibody Biological Activity Against Influenza A HemagglutininElla BarkanIbrahim Siddiquiet al.2025Computational And Structural Biotechnology Journal
Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicityJeffrey K WeberJoseph A Morroneet al.2024Briefings in Bioinformatics
Combining molecular simulation and AI for antibody design against cancer immunotherapy targetsJeff Weber2023ACS Fall 2023
Molecular dynamics as a data source: scaling simulation for building AI modelsJoseph MorroneJeff Weberet al.2023ACS Fall 2023
Graph-based 3D Generative Small-Molecule Modeling Targeting for Multi Proteins with Enhanced Binding CompatibilitySeung Gu KangJeff Weberet al.2023ACS Fall 2023
Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptideXiaolong LiNishant Kumar Singhet al.2023Nature Communications
Predicting HLA-peptide complex immunogenicity with molecular dynamics and graph convolutional deep learningJeff Weber2022ACS Fall 2022
In-Pocket 3D Graphs Enhance Ligand-Target Compatibility in Generative Small-Molecule CreationSeung Gu KangJeff Weberet al.2022arXiv
Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational Autoencoder─Insights for Practical AI-Driven Molecule GenerationSeung-Gu KangJoseph A. Morroneet al.2022J. Chem. Inf. Model.
Simplified, interpretable graph convolutional neural networks for small molecule activity predictionJeffrey K. WeberJoseph A. Morroneet al.2021J. Comput. Aided Mol. Des.