A5049222465- Protein Structure and Dynamics
- Enzyme Structure and Function
- Monoclonal and Polyclonal Antibodies Research
- RNA and protein synthesis mechanisms
- SARS-CoV-2 and COVID-19 Research
- vaccines and immunoinformatics approaches
- Metabolomics and Mass Spectrometry Studies
- T-cell and B-cell Immunology
- Genetics, Bioinformatics, and Biomedical Research
- Biochemical and Structural Characterization
- Immunotherapy and Immune Responses
- Bacteriophages and microbial interactions
- Animal Virus Infections Studies
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
Stanford University
2022-2025
Stanford Medicine
2025
Bioengineering Center
2023
Johns Hopkins University
2022
Proteins mediate their functions through chemical interactions; modeling these interactions, which are typically sidechains, is an important need in protein design. However, constructing all-atom generative model requires appropriate scheme for managing the jointly continuous and discrete nature of proteins encoded structure sequence. We describe diffusion structure, Protpardelle, represents all sidechain states at once as a “superposition” state; superpositions defining collapsed into...
A bstract Proteins mediate their functions through chemical interactions; modeling these interactions, which are typically sidechains, is an important need in protein design. However, constructing all-atom generative model requires appropriate scheme for managing the jointly continuous and discrete nature of proteins encoded structure sequence. We describe diffusion structure, Protpardelle, instantiates a “superposition” over possible sidechain states, collapses it to conduct reverse sample...
The ongoing emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants concern (VOCs) that reduce the effectiveness antibody therapeutics necessitates development next-generation modalities are resilient to viral evolution. Here, we characterized amino-terminal domain (NTD)- and receptor binding (RBD)-specific monoclonal antibodies previously isolated from disease 2019 (COVID-19) convalescent donors for their activity against emergent SARS-CoV-2 VOCs. Among these,...
Many proteins' biological functions rely on interconversions between multiple conformations occurring at micro- to millisecond (μs-ms) timescales. A lack of standardized, large-scale experimental data has hindered obtaining a more predictive understanding these motions. After curating >100 Nuclear Magnetic Resonance (NMR) relaxation datasets, we realized an observable for μs-ms motion was hiding in plain sight. Millisecond motions can cause NMR signals broaden beyond detection, leaving...
Identifying highly specific T cell receptors (TCRs) or antibodies against epitopic peptides presented by class I major histocompatibility complex (MHC I) proteins remains a bottleneck in the development of targeted therapeutics. Here, we introduce recognition antigen–MHC reporter for MHC (TRACeR-I), generalizable platform targeting on polymorphic HLA-A*, HLA-B* and HLA-C* allotypes while overcoming cross-reactivity challenges TCRs. Our TRACeR–MHC co-crystal structure reveals unique antigen...
Abstract Singular value decomposition (SVD) of multiple sequence alignments (MSAs) is an important and rigorous method to identify subgroups sequences within the MSA, extract consensus covariance features that define alignment distinguish subgroups. This information can be correlated structure, function, stability, taxonomy. However, mathematics SVD unfamiliar many in field protein science. Here, we attempt present intuitive yet comprehensive description analysis MSAs. We begin by describing...
Abstract The ongoing emergence of SARS-CoV-2 variants concern (VOCs) that reduce the effectiveness antibody therapeutics necessitates development next-generation modalities are resilient to viral evolution. Here, we characterized N-terminal domain (NTD) and receptor binding (RBD)-specific monoclonal antibodies previously isolated from COVID-19 convalescent donors for their activity against emergent VOCs. Among these, NTD-specific C1596 displayed greatest breadth VOCs, with cryo-EM structural...