MolProbity is implemented in PHP as a web server located at http://molprobity.biochem.duke.edu . It provides a graphical interface to a collection of Richardson lab programs for validation and structure correction. However, MolProbity is not a mere job-submission form; it is a complex web application that offers multiple modes of use, integrates many different kinds of information and suggests courses of action based on that information.
MolProbity uses a variety of physics- and knowledge-based algorithms to analyze a structure. The primary basis of its enhanced effectiveness is all-atom contact analysis, as implemented in Probe (16 (link)). All-atom contacts are exquisitely sensitive to a wide variety of local misfittings, but they are not yet available in other validation systems. They do require explicit hydrogen atoms, but MolProbity can add and optimize these using Reduce (17 (link)), while at the same time detecting and automatically fixing flipped Asn, Gln and His sidechains. MolProbity also uses carefully filtered, high-accuracy Ramachandran and rotamer distributions to check mainchain and sidechains for conformational outliers. Finally, it reports on some novel geometric indicators of misfitting, such as the Cβ deviation (18 (link)) and the base-phosphate perpendicular distance. The different types of analysis are synthesized into two integrated reports on the structural model: one tabular and one graphical.
MolProbity uses a variety of physics- and knowledge-based algorithms to analyze a structure. The primary basis of its enhanced effectiveness is all-atom contact analysis, as implemented in Probe (16 (link)). All-atom contacts are exquisitely sensitive to a wide variety of local misfittings, but they are not yet available in other validation systems. They do require explicit hydrogen atoms, but MolProbity can add and optimize these using Reduce (17 (link)), while at the same time detecting and automatically fixing flipped Asn, Gln and His sidechains. MolProbity also uses carefully filtered, high-accuracy Ramachandran and rotamer distributions to check mainchain and sidechains for conformational outliers. Finally, it reports on some novel geometric indicators of misfitting, such as the Cβ deviation (18 (link)) and the base-phosphate perpendicular distance. The different types of analysis are synthesized into two integrated reports on the structural model: one tabular and one graphical.
