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Protocol
Prediction of Peptide and TCR CDR3 Loops in Formation of Class I MHC-Peptide-TCR Complexes Using Molecular Models with Solvation
Formation of major histocompatibility (MHC)-peptide-T cell receptor (TCR) complexes is central to initiation of an adaptive immune response. These complexes form through initial stabilization of the MHC fold v...
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Protocol
The PANDORA Software for Anchor-Restrained Peptide:MHC Modeling
Major histocompatibility complexes ( ) play a key role in the immune surveillance system in all jawed vertebrates. MHC class molecules randomly sample cytosolic peptides from inside the cell, while MHC class...
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Protocol
Evaluation of Innate Lymphoid Cells and Dendritic Cells Following Viral Vector Vaccination
Recently, we have shown that fate of a vaccine is determined by the cytokine milieu in the innate immune compartment at the early stage of vaccination. Specifically, 24 h post-delivery, level of innate lymphoi...
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Protocol
Antibody Aggregate Removal Using a Mixed-Mode Chromatography Resin
In monoclonal antibody (mAb) production, aggregates represent a major class of product-related impurities that needs to be removed by the downstream process. Protein A chromatography is generally less effectiv...
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Protocol
Flavivirus DNA Vaccine Design and Adjuvant Selection
A DNA vaccine is a plasmid encoding a vaccine antigen together with an efficient eukaryotic promoter to drive protein expression. The chief problem of DNA vaccines has been their suboptimal immunogenicity in h...
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Protocol
Determination of Fraction Unbound and Unbound Partition Coefficient to Estimate Intracellular Free Drug Concentration
Intracellular free drug concentrations are critical to develop pharmacokinetic and pharmacodynamic relationships, estimate therapeutic indices, and predict drug–drug interaction potentials. Free drug concentra...
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Protocol
Contribution of Nontarget Cells to the Disposition, Antitumor Activity, and Antigen-Independent Toxicity of Antibody–Drug Conjugates
After many years of work, antibody–drug conjugates (ADCs) have emerged as an effective strategy for targeting cytotoxic agents to a variety of cancer indications. With nine currently approved ADCs and several ...
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Protocol
Subcellular Drug Depots as Reservoirs for Small-Molecule Drugs
Therapeutic nanoparticles (TNP) have been developed to more efficiently and safely deliver medicines, especially for the treatment of solid cancers. TNP can deliver drugs through extended systemic payload rele...
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Protocol
In Vitro Methodologies to Assess Potential for Transporter-Mediated Drug–Drug Interactions
The importance of membrane transporters and drug-metabolizing enzymes on drug absorption and disposition is widely known. Our current understanding of transporters and enzymes has been achieved largely through...
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Protocol
Solid-State Nanopore for Detecting Individual Biopolymers
Solid-state nanopores have been fabricated and used to characterize single DNA and protein molecules. Here we describe the details on how these nanopores were fabricated and characterized, the nanopore sensing...
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Protocol
MicroPET, MicroSPECT, and NIR Fluorescence Imaging of Biomolecules In Vivo
Molecular imaging is a newly merged multidisciplinary subject that requires contributions from biology, medical physics, and chemistry/radiochemistry. Integrin αvβ3, a cell adhesion molecule, plays pivotal roles ...