V. B. Chen

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.

KiNG and the kinemage interactive three-dimensional graphics it displays are a powerful yet easy to use system for viewing and analysing structures of macromolecules. Kinemages can be used in a variety of ways, from interactive molecular illustrations for teaching or the web, to display of high-dimensional data or detailed structural analysis for research. KiNG also provides a set of crystallographic rebuilding tools, including a novel ‘backrub’ tool for making local, non-disruptive adjustments to protein backbone that couple strongly to side-chain changes, supported by display of electron density, rotamer quality and all-atom contact analysis. KiNG includes a suite of tools for conveniently constructing kinemages from a variety of sources, as well as an extensive set of on-screen editing and drawing functions. Keywords: KiNG; Molikin; Mage; kinemage; molecular graphics; structure validation