ribbon display from Mage

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.

All-atom Contact analysis in Mage

Software: Display & Contacts & Utilities

For 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

Portion of new Ramachandran contours

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:
RLabDuke on GitHub
Out-of-date but still pertinent: Top500 README for info about Ramachandran contours and rotamer scoring.
HiQ54 dataset High Quality for critical methods-testing
RNA backbone rotamers vintage RNA05 (will be superseded by RNA11)

MolProbity Logo slice

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.

Local backbone movements

Research: 3D structure of proteins & nucleic acids

All-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]

Monoclinic SG bears in Mage

Teaching: Course materials

Duke courses: BCH622, BCH681, BCH258 (old), BCH291 (old).
Workshop material: on-line tutorial on MolProbity validation and rebuilding; CSHL X-Ray course practical exercises; and others.

SOD drawing

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.

Duke Chapel and cranes

About us: RLab info and links

Lab 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.