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Kinemages: 3D interactive graphics (QuickStartKiNG documentation)"The Mage Page" discusses the history and of kinemages; some premade kinemage files are in kinemage list, or download section. At the extremes, kinemages can be displayed in immersive virtual reality with Kinimmerse or on mobile-device Safari browsers with Magekinjas. |
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Software: Display & Contacts & UtilitiesFor those working with RNA: Suitename reports on RNA backbone conformers either in MolProbity or standalone. See also links to collaborators' software, such as ERRASER, a thorough RNA backbone correction system. Software source-code, Datasets, and libraries as they evolve are now distributed on GitHub, see RLabDuke on GitHub |
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Structural Informatics: datasets, libraries, etc.
Top8000 dataset (supersedes Top500) which in turn has evolved as we test and apply more strict quality filters. Git repositories "reference_data" and "BJH_Dissertation" hold some of these datasets and libraries. See:
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MolProbity: structure validation, with new H parameters (March 2013)
Web service for all-atom contact, conformation, & geometry analysis of x-ray or NMR models, with automated correction of Asn/Gln/His flips. As a structure user, you can easily evaluate reliability of the parts you care about. |
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Research: 3D structure of proteins & nucleic acidsAll-atom contacts; structure validation & improvement; protein backbone motions; protein sidechain rotamers; RNA backbone rotamers, or explore from the RLab research index page. [Caveat: seldom updated] |
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Teaching: Course materials
Duke courses: BCH622, BCH681, BCH258 (old), BCH291 (old). |
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Gallery: images, etc.Visit Jane's WikiMedia Commons page for macromolecular & other images. View the on-line HTML version (or download PDFs) of the annotated Anatomy and Taxonomy of Protein Structure. Try a small selection of other 2D images. |
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About us: RLab info and linksLab members; directions to the lab; publications: recent, classic, and dissertations; lab links & partners in quality: PHENIX, ROC (RNA Ontology), Duke Biochemistry Dept., SBB Pgm (Structural Biology & Biophysics), CBB Pgm (Computational Biology & Bioinformatics), WikiProject Biophysics. |