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dc.contributor.authorChakraborty, Promitaen_US
dc.date.accessioned2014-05-09T08:01:02Z
dc.date.available2014-05-09T08:01:02Z
dc.date.issued2014-05-08en_US
dc.identifier.othervt_gsexam:2628en_US
dc.identifier.urihttp://hdl.handle.net/10919/47932
dc.description.abstractAlthough nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees-of-freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and alpha-carbon units, connected by mechanical bonds (corresponding to phi and psi angles) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to easily fold into stable secondary structures. This physical model can serve as the basis for linking tangible bio-macromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human-computer interface. We have explored the boundaries of this direction at the interface of computational tools and physical models of biological macromolecules at the nano-scale. Using a CAD-biocomputational framework, we have provided a methodology to design and build physical protein models focusing on shape and dynamics. We have also developed a workflow and an interface implemented for such bio-modeling tools. This physical-digital interface paradigm, at the intersection of native state proteins (P), computational models (C) and physical models (P), provides new opportunities for building an interactive computational modeling tool for protein folding and drug design. Furthermore, this model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure.en_US
dc.format.mediumETDen_US
dc.publisherVirginia Techen_US
dc.rightsThis Item is protected by copyright and/or related rights. Some uses of this Item may be deemed fair and permitted by law even without permission from the rights holder(s), or the rights holder(s) may have licensed the work for use under certain conditions. For other uses you need to obtain permission from the rights holder(s).en_US
dc.subjectPhysical modelsen_US
dc.subjectpolypeptidesen_US
dc.subjectRamachandran ploten_US
dc.subject3D-printingen_US
dc.subjectmolecular modelen_US
dc.subjectprotein foldingen_US
dc.subjectstructural biologyen_US
dc.subjectbiochemistry educationen_US
dc.subjectphysical-digital interfaceen_US
dc.subjectmacromoleculeen_US
dc.subjectPeppytideen_US
dc.titleA Computational Framework for Interacting with Physical Molecular Models of the Polypeptide Chainen_US
dc.typeDissertationen_US
dc.contributor.departmentComputer Scienceen_US
dc.description.degreePh. D.en_US
thesis.degree.namePh. D.en_US
thesis.degree.leveldoctoralen_US
thesis.degree.grantorVirginia Polytechnic Institute and State Universityen_US
thesis.degree.disciplineComputer Science and Applicationsen_US
dc.contributor.committeechairZuckermann, Ronald N.en_US
dc.contributor.committeechairOnufriev, Alexeyen_US
dc.contributor.committeememberRamakrishnan, Narendranen_US
dc.contributor.committeememberZhang, Liqingen_US
dc.contributor.committeememberDerisi, Joseph L.en_US


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