The Richardsons' 3D Protein Structure Laboratory
and Kinemage Home Page


[Home] Kinemages Java Mage Software: [MolProbity] Validation Rotamers FTP 2D Gallery Lab Info [Site Map]
Display Contacts Utility


leucine zipper motif
sidechain packing showing contact dots and hydrogens
Lysine rotamers
Prealbumin portion
MolProbity
  web service for protein structure validation using all-atom contacts and geometrical criteria

The Mage Page
  "kinemage" interactive 3D graphics, usually for molecules
Mage, Prekin, teaching examples, tutorials, links, etc.
Java Mage
  Small kinemages interactive right here on the web
(requires Java enabled in your browser)

Software:  free, open source, multi-platform
  Mage  to display kinemages and
  Prekin  to make them for molecules
  Reduce  to add & optimize hydrogens
  Probe  to calculate all-atom contact dots
  and  others

Validation:
  Model Assessment:
  find clashes, flip amides, check phi, psi's
  Crystallography Tools:
  run Probe with XtalView or O, use our rotamer files with them, etc.

Databases:
  Penultimate Rotamer Library
  sidechain conformations from 240 proteins
1.7 Å or better resolution, with high B and
clashing sidechains omitted.
  Structural Data:
  100 PDB files at 1.7 Å or better resolution,
with all H atoms added & optimized.
  500 PDB files at 1.8 Å or better resolution,
with all H atoms added & optimized.

Entrance to  2-D Picture Gallery

Our Complete  FTP Site

We Welcome Your Feedback!


David C. and Jane S. Richardson

Our Page on the Dept Site: research interests, publications, etc.

The Richardson lab studies the 3-dimensional structure of proteins and the process of folding to that structure, including the de novo design, synthesis, and characterization of novel small proteins. We compare and classify the structural features found in the known protein structures, and develop new methods for visualizing and modeling proteins. A current focus is the use of all-atom contacts to analyze and improve macromolecular structures, including application to structural genomics as part of the SECSG.

Opportunities and research philosophy


211 Nanaline Duke Bldg.
Box 3711 DUMC
Durham, NC 27710
[Note: Use room address for courier deliveries, but for US mail, the "Box 3711" is essential!]
919-684-6010 (office); 919-684-8885 (fax)		 email:
    David Richardson
    Jane Richardson		 Dept. of Biochemistry
Graduate Program in
Molecular Biophysics
Duke University
SouthEast Collaboratory for
Structural Genomics