phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.

The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement

IDSS: deformation invariant signatures for molecular shape comparison

<p>Abstract</p> <p>Background</p> <p>Many molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison (MSC) treat them as rigid bodies, which may lead to incorrect measure of the shape similarity of flexible molecules.</p> <p>Results</p> <p>To address the issue we introduce a new shape descriptor, called Inner Distance Shape Signature (IDSS), for describing the 3D shapes of flexible molecules. The inner distance is defined as the length of the shortest path between landmark points within the molecular shape, and it reflects well the molecular structure and deformation without explicit decomposition. Our IDSS is stored as a histogram which is a probability distribution of inner distances between all sample point pairs on the molecular surface. We show that IDSS is insensitive to shape deformation of flexible molecules and more effective at capturing molecular structures than traditional shape descriptors. Our approach reduces the 3D shape comparison problem of flexible molecules to the comparison of IDSS histograms.</p> <p>Conclusion</p> <p>The proposed algorithm is robust and does not require any prior knowledge of the flexible regions. We demonstrate the effectiveness of IDSS within a molecular search engine application for a benchmark containing abundant conformational changes of molecules. Such comparisons in several thousands per second can be carried out. The presented IDSS method can be considered as an alternative and complementary tool for the existing methods for rigid MSC. The binary executable program for Windows platform and database are available from <url>https://engineering.purdue.edu/PRECISE/IDSS</url>.</p

Rules and Tools in the Battle against Superbugs - A call for integrated strategies and enhanced international collaboration to promote antimicrobial drug development

The lack of treatments during the recent Ebola and Zika outbreaks dramatically exposed the vulnerability of the global health system and the dire consequences thereof. But even where therapies against infectious diseases had been available, an additional threat has gained world-wide attention: antimicrobial resistance (AMR). A growing number of microbial organisms are becoming resistant to available drugs with increasingly diverse risks for a rapid global spreading of infections. Unfortunately, the traditional IP based innovation system and regulatory frameworks do not provide sufficient incentives to invest in the development of new antimicrobials. Hence, there are few new treatments in the pipeline to replace a growing number of ineffective drugs or problematic drug combinations. Repairing these broken economic incentives, improving access to and sustaining the effectiveness of antimicrobials is among the most important challenges in the health and life sciences. In this paper we emphasize that this goal can only be achieved through integrated strategies and a better global coordination of interdisciplinary multi-sector responses