Search

In this work, we present the frontend of GeoMine and showcase its application, focusing on the new features of its latest version. GeoMine is a search engine for ligand-bound and predicted empty binding sites in the Protein Data Bank. In addition to its basic text-based search functionalities, GeoMine offers a geometric query type for searching binding sites with a specific relative spatial arrangement of chemical features such as heavy atoms and intermolecular interactions. In contrast to a text search that requires simple and easy-to-formulate user input, a 3D input is more complex, and its specification can be challenging for users. GeoMine's new version aims to address this issue from the graphical user interface perspective by introducing an additional visualization concept and a new query template type. In its latest version, GeoMine extends its query-building capabilities primarily through input formulation in 2D. The 2D editor is fully synchronized with GeoMine's 3D editor and provides the same functionality. It enables template-free query generation and template-based query selection directly in 2D pose diagrams. In addition, the query generation with the 3D editor now supports predicted empty binding sites for AlphaFold structures as query templates. GeoMine is freely accessible on the ProteinsPlus web server ( https://proteins.plus )., (© 2024. The Author(s).)

In this article, we present PoseEdit, a new, interactive frontend of the popular pose visualization tool PoseView. PoseEdit automatically produces high-quality 2D diagrams of intermolecular interactions in 3D binding sites calculated from ligands in complex with protein, DNA, and RNA. The PoseView diagrams have been improved in several aspects, most notably in their interactivity. Thanks to the easy-to-use 2D editor of PoseEdit, the diagrams are extensively editable and extendible by the user, can be merged with other diagrams, and even be created from scratch. A large variety of graphical objects in the diagram can be moved, rotated, selected and highlighted, mirrored, removed, or even newly added. Furthermore, PoseEdit enables a synchronized 2D-3D view of macromolecule-ligand complexes simplifying the analysis of structural features and interactions. The representation of individual diagram objects regarding their visualized chemical properties, like stereochemistry, and general graphical styles, like the color of interactions, can additionally be edited. The primary objective of PoseEdit is to support scientists with an enhanced way to communicate ligand binding mode information through graphical 2D representations optimized with the scientist's input in accordance with objective criteria and individual needs. PoseEdit is freely available on the ProteinsPlus web server ( https://proteins.plus )., (© 2023. The Author(s).)

Canada is one of the early pioneers of Advance Care Planning concepts, processes, programs and initiatives. The evolution of national messages, models and frameworks is shaped by our publicly funded healthcare system and culturally diverse populations. Our Pan-Canadian Community Framework highlights the importance of individuals, those that matter to them, communities, organizations, and healthcare professionals collaborating, integrating, sharing, and building upon each other's strengths and successes. This framework describes Canada's priority actions at national, provincial and local levels. Our collective vision is for Advance Care Planning to be a part of the life journey., (Copyright © 2023. Published by Elsevier GmbH.)

Background: Long-term care (LTC) homes have been disproportionately impacted during COVID-19., Purpose: To explore the perspectives of stakeholders across Canada around implementing a palliative approach in LTC home during COVID-19., Methods: Qualitative, descriptive design using one-to-one or paired semi-structured interviews., Results: Four themes were identified: (1) the influence of the pandemic on implementing a palliative approach, (2) families are an essential part of implementing a palliative approach, (3) prioritizing advance care planning (ACP) and goals of care (GoC) discussions in anticipation of the overload of deaths and (4) COVID-19 highlighting the need for a palliative approach as well as several subthemes., Conclusion: The COVID-19 pandemic influenced the implementation of a palliative approach to care, where many LTC homes faced an overwhelming number of deaths and restricted the presence of family members. A more concentrated focus on home-wide ACP and GoC conversations and the need for a palliative approach to care in LTC were identified., (© 2023. The Author(s).)

Upon the ever-increasing number of publicly available experimentally determined and predicted protein and nucleic acid structures, the demand for easy-to-use tools to investigate these structural models is higher than ever before. The ProteinsPlus web server (https://proteins.plus) comprises a growing collection of molecular modeling tools focusing on protein-ligand interactions. It enables quick access to structural investigations ranging from structure analytics and search methods to molecular docking. It is by now well-established in the community and constantly extended. The server gives easy access not only to experts but also to students and occasional users from the field of life sciences. Here, we describe its recently added new features and tools, beyond them a novel method for on-the-fly molecular docking and a search method for single-residue substitutions in local regions of a protein structure throughout the whole Protein Data Bank. Finally, we provide a glimpse into new avenues for the annotation of AlphaFold structures which are directly accessible via a RESTful service on the ProteinsPlus web server., (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.)