Molecular conformational sampling using collective coordinate expansive spaces

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dc.contributor.advisorKavraki, Lydia E.
dc.creatorTeodoro, Miguel L.
dc.date.accessioned2009-06-04T06:35:16Z
dc.date.available2009-06-04T06:35:16Z
dc.date.issued2004
dc.description.abstractPoor conformational sampling is the most significant problem in determining stable molecular conformations and free energy changes in molecular systems. This problem is particularly difficult for large molecules such as proteins for which the dimensionality of the conformational space can be of thousands of degrees of freedom. In this work we describe a new method, collective coordinate expansive spaces, for efficient conformational sampling of molecules. The new method performs a dimensional reduction of the molecular system using principal components analysis in dihedral space. The reduced dimensionality representation is subsequently used for conformational sampling by means of a randomized exploration technique. The new method was tested for conformational sampling of four different molecular systems and compared to existing sampling methods. The initial conformational dimensionality of the model systems ranged from 8 to 228 degrees of freedom. The new method displayed the best conformational coverage for systems larger than 36 degrees of freedom.
dc.format.extent65 p.en_US
dc.format.mimetypeapplication/pdf
dc.identifier.callnoTHESIS BIOCHEM. 2004 TEODORO (M.S.)
dc.identifier.citationTeodoro, Miguel L.. "Molecular conformational sampling using collective coordinate expansive spaces." (2004) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/17736">https://hdl.handle.net/1911/17736</a>.
dc.identifier.urihttps://hdl.handle.net/1911/17736
dc.language.isoeng
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.
dc.subjectBiophysics
dc.subjectComputer science
dc.titleMolecular conformational sampling using collective coordinate expansive spaces
dc.typeThesis
dc.type.materialText
thesis.degree.departmentBiochemistry and Cell Biology
thesis.degree.disciplineNatural Sciences
thesis.degree.grantorRice University
thesis.degree.levelMasters
thesis.degree.nameMaster of Science
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