Notes

Preoperative magnetic resonance photo criteria regarding projecting lymph node metastasis throughout patients with stage IB1-IIA2 cervical cancers.
After several seconds of adaptation to a visual array of randomly oriented Gabor patterns, observers can detect and localise a change in the orientation of one of these Gabors, even when the change is preceded by a blank inter-stimulus interval. Previously, we reported that the ability to detect this changed element was unaffected by distracting observers' attention away from the adapting stimuli by making them look for rare conjunctions of shape and colour at the central fixation point. That finding is replicated in the current paper, and augmented by a demonstration of the attentionally demanding nature of the conjunction search it significantly impairs discrimination between adapting arrays in which either many or few items briefly lose contrast. Consequently, we can be certain of adaptation's immunity to the withdrawal of attention, when assessed objectively (i.e. with a performance-based metric).Augmented reality (AR) allows a computer-generated 3D model to be superimposed onto a real-world environment in real time. The model can then be manipulated or probed interactively as if it is part of the real world. The application of AR in visualizing macromolecular structures is growing, primarily in showing preset collections of scenes for education purpose. Here, our emphasis is, however, on exploiting AR as a tool to facilitate scientific communication on the go. We have searched for freely available mobile software and custom-built tools which allow the display of user-specified protein structures. We provide step-by-step guides on a standalone app Ollomol (iOS and Android), as well as an in-browser web app, WebAR-PDB. Both of them allow users to specify entries from the Protein Data Bank (PDB) for an elementary AR experience. The application of AR enhances interactivity and imaginativity in macromolecular visualization.With the rise of tablets, truly portable molecular graphics are now available for wide use by scientists to share structural information in real time. We have surveyed the existing software available on Apple iPads and on Android tablets in order to make a recommendation to potential users, primarily based on the product features. Among the three apps for high-quality 3-D display, iMolview (available on both platforms) stands out to be our choice, with PyMOL app (iOS) a close alternative and NDKmol (Android) offering some uniquely useful functions. Hence we include a tutorial on how to get started using iMolview to do some simple visualization in 10 min.Enhancement of proteins by PEGylation is an active area of research. However, the interactions between polymer and protein are far from fully understood. To gain a better insight into these interactions or even make predictions, molecular dynamics (MD) simulations can be applied to study specific protein-polymer systems at molecular level detail. Here we present instructions on how to simulate PEGylated proteins using the latest iteration of the Martini coarse-grained (CG) force-field. CG MD simulations offer near atomistic information and at the same time allow to study complex biological systems over longer time and length scales than fully atomistic-level simulations.Fluorescent labeling of protein has been widely used in microbiology for detection and analysis. Molecular dynamics simulations provide vital supporting information for predictions and interpretations of experimental results. While force fields for proteins with regular amino acids are readily available, parameters for covalently attached fluorophores have to be incorporated into these force fields before they can be used for simulations. In this chapter, we shall discuss the methods to parameterize a fluorescent probe (fluorescein) attached to a cysteine, as a modified residue, for performing simulations with GROMACS.Molecular dynamics (MD) simulation is a powerful method of investigating the interaction between molecular species. Defining the mechanical properties and topologies for all components involved is critical. While parameters for proteins are well established, those for the wide range of ligands and substrates are not. Here we introduce a very useful service which is designed for small organic molecules. We describe a protocol to extend this tool to beyond its current size (200 atoms) and formal charge (2+ to 2-) limits.The MCPB.py program greatly facilitates force field parameterization for metal sites in metalloproteins and organometallic compounds. Herein we present an example of MCPB.py to the parameterization of the dioxygen binding metal site of peptidylglycine-alphahydroxylating monooxygenase (PHM), which contains a copper ion. In this example, we also extend the functionality of MCPB.py to support molecular dynamics (MD) simulations in GROMACS through a python script. Illustrative MD simulations were performed using GROMACS and the results were analyzed. selleck compound Notes about the program were also provided in this chapter, to assist MCPB.py users for metal site parameterizations.Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.Efficient and comprehensive data management is an indispensable component of modern scientific research and requires effective tools for all but the most trivial experiments. The LabDB system developed and used in our laboratory was originally designed to track the progress of a structure determination pipeline in several large National Institutes of Health (NIH) projects. While initially designed for structural biology experiments, its modular nature makes it easily applied in laboratories of various sizes in many experimental fields. Over many years, LabDB has transformed into a sophisticated system integrating a range of biochemical, biophysical, and crystallographic experimental data, which harvests data both directly from laboratory instruments and through human input via a web interface. The core module of the system handles many types of universal laboratory management data, such as laboratory personnel, chemical inventories, storage locations, and custom stock solutions. LabDB also tracks various biochemical experiments, including spectrophotometric and fluorescent assays, thermal shift assays, isothermal titration calorimetry experiments, and more.
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