Molecular docking and structural analysis for applications in biomedicine

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dc.contributor.advisorKavraki, Lydia Een_US
dc.creatorHall-Swan, Sarahen_US
dc.date.accessioned2023-08-09T16:59:51Zen_US
dc.date.available2023-08-09T16:59:51Zen_US
dc.date.created2023-05en_US
dc.date.issued2023-04-12en_US
dc.date.submittedMay 2023en_US
dc.date.updated2023-08-09T16:59:51Zen_US
dc.description.abstractThe discovery of new drugs and treatments can be facilitated by developing in silico tools. These new methods can guide in vitro experiments and elucidate immune mechanisms via sequence and structural analysis of biomolecules. For immunotherapy treatments, of particular interest are peptide-HLA class I (pHLA) complexes and T-cell receptors (TCRs), which play a crucial role in the immune response against viral infections and cancer. T-cell cross-reactivity, the ability of a single TCR to bind and respond to multiple pHLAs, is a significant aspect of T-cells. Predicting T-cell cross-reactivity can aid in the development of safer cancer immunotherapies and more effective viral vaccines. To this end, we first present PepSim, a novel scoring method that predicts T-cell cross-reactivity based on pHLA similarity. Our method, which is also implemented in a web-based tool, accurately distinguishes between cross-reactive and non-cross-reactive pHLAs across multiple datasets and can be utilized with any class I peptide-HLAs. Next, we leverage PepSim to identify potential vaccine targets against SARS-CoV-2 that may be cross-reactive with other SARS-CoV-2 peptides, thereby offering protection against numerous viral variants. Furthermore, we have created DINC-COVID, an ensemble docking tool that facilitates the development of SARS-CoV-2 drug therapies by taking into account ligand and receptor flexibility and generating plausible binding modes for SARS-CoV-2 proteins.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationHall-Swan, Sarah. "Molecular docking and structural analysis for applications in biomedicine." (2023) Diss., Rice University. <a href="https://hdl.handle.net/1911/115124">https://hdl.handle.net/1911/115124</a>.en_US
dc.identifier.urihttps://hdl.handle.net/1911/115124en_US
dc.language.isoengen_US
dc.rightsCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.en_US
dc.subjectT cell cross-reactivityen_US
dc.subjectmolecular dockingen_US
dc.subjectpeptide-HLAen_US
dc.titleMolecular docking and structural analysis for applications in biomedicineen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentComputer Scienceen_US
thesis.degree.disciplineEngineeringen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
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