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[Protein-ligand docking]
GalaxyDock-DL: Protein–Ligand Docking by Global Optimization and Neural Network Energy. bioRxiv (2024)
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[Antibody design]
Accurate antibody loop structure prediction enables zero-shot design of target-specific antibodies. bioRxiv (2024)
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[Enzyme discovery]
Discovery of Highly Active Kynureninases for Cancer Immunotherapy through Protein Language Model. bioRxiv (2024)
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[Protein-ligand docking for heme proteins]
GalaxyDock2-HEME: Protein-ligand docking for heme proteins, Journal of Computational Chemistry (2023)
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[Protein-ligand docking by alignment with template structures]
CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein–ligand docking, Computational and Structural Biotechnology Journal (2023)
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[Binding site prediction in human proteome]
HProteome-BSite: predicted binding sites and ligands in human 3D proteome, Nucleic Acids Research (2022)
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[Prediction of water positions on protein structures]
GalaxyWater-CNN: Prediction of Water Positions on the Protein Structure by a 3D-Convolutional Neural Network, Journal of Chemical Information and Modeling (2022)
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[Web server for protein domain-domain interaction]
GalaxyDomDock: An Ab Initio Domain–domain Docking Web Server for Multi-domain Protein Structure Prediction, Journal of Molecular Biology (2022)
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[Opinion about recent progress in protein structure prediction]
Accurate protein structure prediction: what comes next?, BioDesign (2021)
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[Invited article from CASP14 in the oligomer structure prediction category]
Protein oligomer structure prediction using GALAXY in CASP14, Proteins (2021)
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[CASP14 assessment article in the accuracy estimation category]
Assessment of Protein Model Structure Accuracy Estimation in CASP14: Old and New Challenges, Proteins (2021)
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[Web server for protein heteromer structure prediction]
GalaxyHeteromer: protein heterodimer structure prediction by template-based and ab initio docking, Nucleic Acids Research (2021)
