Shi, Jiye

SAbDab: the structural antibody database

Dunbar, J., Krawczyk, K., Leem, J., Baker, T., Fuchs, A., Georges, G., Shi, J., & Deane, C. M. (2014) · Nucleic Acids Research

Monoclonal and Polyclonal Antibodies ResearchEnzyme Structure and Function

Cited by 674

Five computational developability guidelines for therapeutic antibody profiling

Raybould, M. I. J., Marks, C., Krawczyk, K., Taddese, B., Nowak, J., Lewis, A. P., Bujotzek, A., Shi, J., & Deane, C. M. (2019) · Proceedings of the National Academy of Sciences

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 357

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Jansen, J., Reimer, K. C., Nagai, J. S., Varghese, F. S., Overheul, G. J., de Beer, M., Roverts, R., Daviran, D., Fermin, L. A. S., Willemsen, B., et al. (2022) · Cell Stem Cell

COVID-19 Clinical Research StudiesSARS-CoV-2 and COVID-19 Research

Cited by 259

DNA Hydrogel with Aptamer-Toehold-Based Recognition, Cloaking, and Decloaking of Circulating Tumor Cells for Live Cell Analysis

Song, P., Ye, D., Zuo, X., Li, J., Wang, J., Liu, H., Hwang, M. T., Chao, J., Su, S., Wang, L., et al. (2017) · Nano Letters

Advanced biosensing and bioanalysis techniquesHydrogels: synthesis, properties, applications

Cited by 258

ABodyBuilder: automated antibody structure prediction with data-driven accuracy estimation

Leem, J., Dunbar, J., Georges, G., Shi, J., & Deane, C. M. (2016) · mAbs

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 238

Thera-SAbDab: the therapeutic structural antibody database

Raybould, M. I. J., Marks, C., Lewis, A. P., Shi, J., Bujotzek, A., Taddese, B., & Deane, C. M. (2020) · Nucleic Acids Research

Monoclonal and Polyclonal Antibodies ResearchEnzyme Structure and Function

Cited by 199

Improving B-cell epitope prediction and its application to global antibody–antigen docking

Krawczyk, K., Liu, X., Baker, T., Shi, J., & Deane, C. M. (2014) · Bioinformatics

vaccines and immunoinformatics approachesProtein Structure and Dynamics

Cited by 174

DNA origami cryptography for secure communication

Zhang, Y., Wang, F., Chao, J., Xie, M., Liu, H., Pan, M., Kopperger, E., Liu, X., Li, Q., Shi, J., et al. (2019) · Nature Communications

DNA and Biological ComputingAdvanced biosensing and bioanalysis techniques

Cited by 163

ABangle: characterising the VH-VL orientation in antibodies

Dunbar, J., Fuchs, A., Shi, J., & Deane, C. M. (2013) · Protein Engineering Design and Selection

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 125

The H3 loop of antibodies shows unique structural characteristics

Regep, C., Georges, G., Shi, J., Popovic, B., & Deane, C. M. (2017) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 99

Analysis and modeling of the variable region of camelid single-domain antibodies

Sircar, A., Sanni, K. A., Shi, J., & Gray, J. J. (2011) · The Journal of Immunology

Monoclonal and Polyclonal Antibodies ResearchProtein Structure and Dynamics

Cited by 92

Antibody i-Patch prediction of the antibody binding site improves rigid local antibody–antigen docking

Krawczyk, K., Baker, T., Shi, J., & Deane, C. M. (2013) · Protein Engineering Design and Selection

Protein Structure and Dynamicsvaccines and immunoinformatics approaches

Cited by 87

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction

Marks, C., Nowak, J., Klostermann, S., Georges, G., Dunbar, J., Shi, J., Kelm, S., & Deane, C. M. (2017) · Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 56

Structurally mapping antibody repertoires

Krawczyk, K., Kelm, S., Kovaltsuk, A., Galson, J. D., Kelly, D., Trück, J., Regep, C., Leem, J., Wong, W. K., Nowak, J., et al. (2018) · Frontiers in Immunology

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 42

Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping

Liu, X., Taylor, R. D., Griffin, L., Coker, S.-F., Adams, R., Ceska, T., Shi, J., Lawson, A. D. G., & Baker, T. (2017) · Scientific Reports

Monoclonal and Polyclonal Antibodies ResearchProtein Structure and Dynamics

Cited by 39

A quantum mechanics-based halogen bonding scoring function for protein-ligand interactions.

Yang, Z., Liu, Y., Chen, Z., Xu, Z., Shi, J., Chen, K., & Zhu, W. (2015) · Journal of Molecular Modeling

Computational Drug Discovery MethodsCrystallography and molecular interactions

Cited by 23

Antibody side chain conformations are position-dependent

Leem, J., Georges, G., Shi, J., & Deane, C. M. (2018) · Proteins Structure Function and Bioinformatics

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 22