dc.creator | Lemmon, Gordon Howard | |
dc.date.accessioned | 2020-08-22T21:13:01Z | |
dc.date.available | 2012-10-15 | |
dc.date.issued | 2012-10-15 | |
dc.identifier.uri | https://etd.library.vanderbilt.edu/etd-10152012-130148 | |
dc.identifier.uri | http://hdl.handle.net/1803/14316 | |
dc.description.abstract | Structure-based drug design is a key challenge for pharmaceutical chemists. By studying the structure of proteins bound to natural substrates, researchers can design small molecules which they predict will bind in a similar fashion. Ligand docking software such as RosettaLigand plays a key role in structure-based drug design by predicting how a small molecule and a protein will interact. In this body of research I present improvements to the RosettaLigand docking algorithm. I first demonstrate a strategy for achieving accurate predictions of HIV-1 protease/protease inhibitor binding affinity. Next I present a tutorial for using a new version of RosettaLigand docking code which I wrote. This new version allows simultaneous docking of multiple ligands, docking with interface design, and uses an XML-script interface. The XML interface allows fully customizable ligand docking protocols. Finally I demonstrate simultaneous docking of waters along with small molecule inhibitors within protein interfaces. Water docking improves Rosetta’s ability to predict the structure of the protein/inhibitor interface. | |
dc.format.mimetype | application/pdf | |
dc.subject | macromolecular modeling | |
dc.subject | computational biology | |
dc.subject | strutural biology | |
dc.title | Development of methods for docking and designing small molecules within the Rosetta code framework | |
dc.type | dissertation | |
dc.contributor.committeeMember | Brian Bachmann | |
dc.contributor.committeeMember | Jarrod Smith | |
dc.contributor.committeeMember | Richard D'Aquila | |
dc.type.material | text | |
thesis.degree.name | PHD | |
thesis.degree.level | dissertation | |
thesis.degree.discipline | Chemical and Physical Biology | |
thesis.degree.grantor | Vanderbilt University | |
local.embargo.terms | 2012-10-15 | |
local.embargo.lift | 2012-10-15 | |
dc.contributor.committeeChair | David Tabb | |