All-atom Contact Analysis Tutorial, Introduction

Structure Validation WorkshopUsing All-Atom Contact Analysis for ModelDiagnosis & RepairThis three-part tutorial is intended as a self-paced (although we use the practicals forworkshops), self-guided introduction to using all-atom contacts in macromolecule building andrefinement. While you will be introduced to a powerful toolset, there are other tools available, andwe invite you to explore them on our website (http://kinemage.biochem.duke.edu/).Parts of the practical -- The tutorial lessons:1. Add H, calculate contacts, and assess geometry by running the MolProbity web service.2. Repair of problem sidechains using the interactive KiNG/Probe system3. Local backbone adjustments using KiNGThe HTML pages, associated image files and datafiles (coordinate files, kinemage files, andmaps) comprising this tutorial can be downloaded as a zip archive.Reprint PDFs & Other"The penultimate rotamer library." Proteins, 2000 New rotamer library (the one of stereochemduke.odb)"Structure validation by C-alpha geometry: phi, psi and C-beta deviation." Proteins, 2003 updates Ramachandran plot contours and introduces the C-beta-deviation measure"New tools and data for improving structures, using all-atom contacts." All-atom contact methodology applied to crystallography; from Methods In Enzymology,Vol. 374"A test of enhancing model accuracy in high-throughput crystallography." JSFG, 2005 Statistics showing large improvements using these tools.All-atom contact ...