PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDS

University Of Calif-Lawrenc Berkeley Lab, Berkeley CA

Investigators

Linked publications & trials

Abstract

The overall PHENIX project seeks to create an integrated platform for rapid development of new methods in[unreadable] automated structure solution, resulting in a software system that can go from experimental x-ray diffraction[unreadable] data all the way to a minimally biased final model. Structure validation (evaluating global and local accuracy[unreadable] of the molecular model) is a required part of such a process. Even more importantly, if the validation criteria[unreadable] are available within the PHENIX system, they can help improve automated decision-making throughout the[unreadable] process. The Duke group developed kinemage graphics, pioneered all-atom contact analysis as a powerful[unreadable] new source of independent validation information, introduced new validation criteria for RNA, and[unreadable] significantly updated the traditional conformational criteria for proteins. This makes the MolProbity web[unreadable] service and related software the most complete system available for diagnosing and then actually correcting[unreadable] problems in macromolecular models, and these methods are well-suited to adaptation and automation within[unreadable] PHENIX. Project V will collaboratively pursue the following research aims: a) provide all-atom contact,[unreadable] geometrical, and other quality criteria within PHENIX, both at a high level for users and at a low level as[unreadable] functions directly accessible by the other software components; b) for the nucleic-acid tool development,[unreadable] contribute quality-filtered fragment libraries, RNA backbone rotamers, conformational inference from the[unreadable] best-determined map features, and new validation measures; c) for refinement and model completion,[unreadable] develop new strategies based on automation of MolProbity structure corrections, refinement of hydrogen[unreadable] atom contacts, and construction of rotameric-ensemble models; d) develop custom 3D and 2D kinemage[unreadable] graphics to display results and alternatives at chosen stages throughout the PHENIX process.