Show simple item record

Novel Computational Protein Design Algorithms with Applications to Cystic Fibrosis and HIV

dc.contributor.advisor Donald, Bruce R
dc.contributor.author Roberts, Kyle Eugene
dc.date.accessioned 2014-08-27T15:20:51Z
dc.date.available 2016-08-17T04:30:03Z
dc.date.issued 2014
dc.identifier.uri https://hdl.handle.net/10161/9041
dc.description.abstract <p>Proteins are essential components of cells and are crucial for catalyzing reactions, signaling, recognition, motility, recycling, and structural stability. This diversity of function suggests that nature is only scratching the surface of protein functional space. Protein function is determined by structure, which in turn is determined predominantly by amino acid sequence. Protein design aims to explore protein sequence and conformational space to design novel proteins with new or improved function. The vast number of possible protein sequences makes exploring the space a challenging problem. </p><p>Computational structure-based protein design (CSPD) allows for the rational design of proteins. Because of the large search space, CSPD methods must balance search accuracy and modeling simplifications. We have developed algorithms that allow for the accurate and efficient search of protein conformational space. Specifically, we focus on algorithms that maintain provability, account for protein flexibility, and use ensemble-based rankings. We present several novel algorithms for incorporating improved flexibility into CSPD with continuous rotamers. We applied these algorithms to two biomedically important design problems. We designed peptide inhibitors of the cystic fibrosis agonist CAL that were able to restore function of the vital cystic fibrosis protein CFTR. We also designed improved HIV antibodies and nanobodies to combat HIV infections.</p>
dc.subject Bioinformatics
dc.subject Biophysics
dc.subject Biochemistry
dc.subject Continuous Rotamers
dc.subject Cystic Fibrosis
dc.subject HIV Neutralization
dc.subject Peptide Inhibitors
dc.subject Protein Design
dc.subject Provable Algorithms
dc.title Novel Computational Protein Design Algorithms with Applications to Cystic Fibrosis and HIV
dc.type Dissertation
dc.department Computational Biology and Bioinformatics
duke.embargo.months 24


Files in this item

Thumbnail

This item appears in the following Collection(s)

Show simple item record