Structural Biology & Biophysics Program @ Duke University

MolProbity structure validation and correction service

Web service for all-atom contact and geometrical analysis of macromolecular coordinate models.

MolProbity is a general-purpose web server offering quality validation for 3D structures of proteins, nucleic acids and complexes. It provides detailed all-atom contact analysis of any steric problems within the molecules as well as updated dihedral-angle diagnostics, and it can calculate and display the H-bond and van der Waals contacts in the interfaces between components. An integral step in the process is the addition and full optimization of all hydrogen atoms, both polar and nonpolar. New analysis functions have been added for RNA, for interfaces, and for NMR ensembles. Additionally, both the web site and major component programs have been rewritten to improve speed, convenience, clarity and integration with other resources. MolProbity results are reported in multiple forms: as overall numeric scores, as lists or charts of local problems, as downloadable PDB and graphics files, and most notably as informative, manipulable 3D kinemage graphics shown online in the KiNG viewer. This service is available free to all users at http://molprobity.biochem.duke.edu.

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.

Protein Folding Funnel Functions: Mathematica images, scripts...

The Duke Magnetic Resonance Spectroscopy Center (DMRSC) 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.

Macromolecular X-ray Crystallography Resource

Duke has a fully-equipped state-of-the-art X-ray crystallography facility that is located in the Levine Science Research Center (LSRC). The facility includes: two Rigaku area detectors, two Rigaku X-ray generators with mirror optics, a computer control room where diffraction data is processed, a wet lab where crystal trays can be set up, and two constant-temperature rooms with vibration-isolated platforms where crystals are grown. A full-time PhD-level manager maintains the equipment and provides assistance with data collection and structure determination.

Protein Data Bank (PDB) depositions by SBB affiliated students