Structural Biology & Biophysics Program @ Duke University
SBB depot: online Web Resources and Content, and Shared Research Facilities
Offerings to the world, of Duke Structural Biology and Biophysics related material.
The MolProbity web service uses all-atom contacts (with H atoms), conformation (rotamers, Ramachandran, & RNA backbone conformers), & covalent geometry criteria to do comprehensive structure validation and improvement. The results are served up as summary scores, as lists of local problems, as downloadable PDB and graphics files, and most notably as markup on interactive 3D kinemage graphics shown online in the KiNG viewer. MolProbity is now the most widely used x-ray structure validation, and its unique measures have improved by about 20% so far in new deposits to the Protein Data Bank worldwide. Several MolProbity criteria are recommended by the PDB's Validation Task Force, for official adoption. The web service, the reference datasets, and all of the related data analysis and graphics software are available free at the Richardson Lab web site.
The Zhou Group develops software to aid in NMR studies of proteins. At present, they have released the PACES program for semi-automated sequential assignment, the PR-CALC package providing all of the needed tools for projection-reconstruction NMR, as well as a C++ library for access to and manipulation of NMR spectral data in the most common file formats.
The Donald Lab develops software both for NMR methodology and for protein design. RDC-Panda provides exact solutions for NMR ensemble structures from two sets of RDC data and minimal NOEs. OSPREY is a protein design package, incorporating provable algorithms for generating a gap-free list of lowest-energy conformations, with features for ensemble evaluation, sidechain rotamer optimization, and various systems for backbone flexibility.
Protein Folding Funnel Functions: Mathematica images, scripts... from the Oas Lab. Also a movie of a linked series of "RUF" domains (Rapidly Unfolding and Folding) using that feature to move through a membrane.
The Erickson lab Lab maintains a resource page of information, based primarily on electron microscopy, about microtubule and extracellular matrix proteins. It includes detailed molecular models, movies, and pictures; genome occurrence and sequence alignments; expression protocols; and assorted goodies like tutorials on RasMol and on PMC IDs.
Many SBB-related visual images of molecular structure are publicly available on the Dcrjsr user page at Wikimedia Commons.
Quick, high-quality, reasonably priced scientific posters are available from PhD Posters, a thriving business founded and operated by SBB students.
The PHENIX crystallographic software system integrates MolProbity validation into both the automated procedures and the user interface. The Richardson Lab is one of the current four developer teams for PHENIX, along with Lawrence Berkeley Lab, Los Alamos, and Cambridge University UK.
The Duke Magnetic Resonance Spectroscopy Center (DMRSC) is directed by SBB faculty member Len Spicer. It provides access to highfield NMR instrumentation, training in the use of NMR methods, and expert consultation on advanced NMR applications. The Center serves as a research resource and shared instrument facility for research programs at Duke and in the Southeastern region. Seven highfield, high resolution NMR spectrometers are supported by the Center and available for use at the present time.
The Duke University Free Electron Laser Lab is directed by SBB faculty member Glenn Edwards. It can produce extremely intense, extremely short pulses of coherent light, and is used for biological and medical research as well as for physics and materials science research.
The Duke Macromolecular X-ray Crystallography Shared Resource
is fully equipped for macromolecular crystallization, crystal screening, X-ray data collection, data processing and structure determination. The facility has newly built state-of-the-art instrumentation including a MicroMax-007 micro focus rotating anode generator and a RAXIS IV++ image plate, equipped with VariMax HR optics and an X-stream 2000 cryogenic system. The X-ray system is completely shielded by a plexiglass enclosure and protected with electronic keypad security. The integrated robotics platform for protein crystallization, consisting of a Phoenix RE, an Alchemist II, and a Minstrel HT Imaging System with two Gallery 700 Incubators, automates every step from protein to crystal. A professional (PhD) crystallographer maintains the facility and provides assistance with crystallization, data collection, and structure determination.
Protein Data Bank (PDB) depositions by SBB affiliated students in recent years has overwhelmed our capacity to update this SBB website, look ,e.g., for mentor and/or student names on the PDB website.