Stochastic Roadmap Simulation: An Efficient Representation and Algorithm for Analyzing Molecular Motion

10.1089/10665270360688011Journal of Computational Biology103-4257-281JCOB

Using Stochastic Roadmap Simulation to predict experimental quantities in protein folding kinetics: Folding rates and phi-values

10.1089/cmb.2007.R004Journal of Computational Biology145578-593JCOB

Stochastic conformational roadmaps for computing ensemble properties of molecular motion

10.1007/978-3-540-45058-0_9Springer Tracts in Advanced Robotics7 STAR131-14

First imported coccidioidomycosis in Turkey: a potential health risk for laboratory workers outside endemic areas

Coccidioidomycosis caused by Coccidioides immitis or Coccidioides posadasii is endemic in arid climate zones in America, travel-related cases have been reported. We report the first documented case of coccidioidomycosis in Turkey, overviewing reported cases in Europe and underlying difficulties of differential diagnosis outside endemic regions. The patient was an otherwise healthy 41-year-old man who travelled endemic areas. Laboratory diagnosis was based on direct microscopy of two subsequent subcutaneous biopsy specimens and culture and confirmed molecularly. Laboratory personnel should become aware that BioSafety Level-3 organisms may become more frequent and widespread

MORPH-PRO: a novel algorithm and web server for protein morphing

Abstract Background Proteins are known to be dynamic in nature, changing from one conformation to another while performing vital cellular tasks. It is important to understand these movements in order to better understand protein function. At the same time, experimental techniques provide us with only single snapshots of the whole ensemble of available conformations. Computational protein morphing provides a visualization of a protein structure transitioning from one conformation to another by producing a series of intermediate conformations. Results We present a novel, efficient morphing algorithm, Morph-Pro based on linear interpolation. We also show that apart from visualization, morphing can be used to provide plausible intermediate structures. We test this by using the intermediate structures of a c-Jun N-terminal kinase (JNK1) conformational change in a virtual docking experiment. The structures are shown to dock with higher score to known JNK1-binding ligands than structures solved using X-Ray crystallography. This experiment demonstrates the potential applications of the intermediate structures in modeling or virtual screening efforts. Conclusions Visualization of protein conformational changes is important for characterization of protein function. Furthermore, the intermediate structures produced by our algorithm are good approximations to true structures. We believe there is great potential for these computationally predicted structures in protein-ligand docking experiments and virtual screening. The Morph-Pro web server can be accessed at http://morph-pro.bioinf.spbau.ru

Environmental Informatics for Solid and Hazardous Waste Management: Advances, Challenges, and Perspectives

Environmental informatics has experienced extraordinarily rapid progress in the past decade and has made an invaluable contribution to planning, design, and operations for waste management. In many cases, however, the roles of these information technologies have been limited to stand-alone projects without synergistic effects. This article presents a holistic view and an in-depth discussion of environmental informatics applied to solid and hazardous waste management from the onset to the present status, and to future trends aiming to advance the management potential. With regard to building, maintaining, and developing knowledge-based or artificial intelligence systems, the spectrum of environmental informatics for solid and hazardous waste management can be classified into five categories: database system, geographical information system, decision support system, expert system, and integrated environmental information system. Supporting technologies in the integrated environmental information system can be further divided into five classes in a logical order to enhance understanding: data acquisition, data communication, data and knowledge storage, data mining and knowledge discovery, and data and knowledge utilization. This critical review article may help create sustainable development strategies from a local solution to global opportunities that will elevate environmental informatics to a new level in dealing with more complex problems and large-scale applications for integrated solid and hazardous waste management. © 2013 Copyright Taylor and Francis Group, LLC