structureViz is a Cytoscape plug-in that links the visualization of biological networks provided by Cytoscape with the visualization and analysis of macromolecular structures and sequences provided by UCSF Chimera. When combined with Cytoscape and Chimera, structureViz provides the first tool that links these two critical aspects of computational analysis in a straightforward manner. structureViz includes commands to open structures in Chimera and align them using Chimera's sequence-structure analysis tools. When a structure is opened, structureViz provides an alternative interface to Chimera: the Cytoscape Molecular Structure Navigator. This interface uses a tree-based paradigm to allow users to select and affect the display of models, chains and residues, mostly through the use of context menus.
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| http://dx.doi.org/10.1093/bioinformatics/btm329 | DOI Listing |
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Purification, characterization, optimization, and docking simulation of alkaline protease produced by Brevibacillus agri SAR25 using fish wastes as a substrate.
Food Chem
January 2025
Department of Molecular Biology and Genetics, Faculty of Science, Ataturk University, 25240, Erzurum, Turkey. Electronic address:
Recycling of protein-rich environmental wastes and obtaining more valuable products from these recycled products is a topic of interest for researchers. This study aims to produce, purify, and characterize the physicochemical and structural properties of the protease enzyme produced from Brevibacillus agri SAR25 using salmon fish waste as substrate and also to evaluate the effect of protease on the chicken feather, enzyme-ligand interactions, and active site surface area. The production of protease was optimum on 50 g/L fish waste, pH 8, 40 °C, 96 h, and 150 rpm.
View Article and Find Full Text PDFIn Silico Evaluation of Potential NDM-1 Inhibitors: An Integrated Docking and Molecular Dynamics Approach.
Pharmaceuticals (Basel)
December 2024
Facultad de Ingeniería y Ciencias Básicas, Fundación Universitaria Los Libertadores, Cra. 16 No. 63a-68, Bogotá 111221, Colombia.
Non-fermenting Gram-negative bacteria are resistant to most antibiotics, due to the production of enzymes such as NDM-1. Faced with this challenge, computational methods have become essential for the design of NDM-1 carbapenemase inhibitors, optimizing both the time and cost of the development of new lead molecules. In this study, molecular docking and molecular dynamics (MD) simulations were performed in order to identify effective inhibitors against the NDM-1 enzyme.
View Article and Find Full Text PDFDesign, synthesis, biological and evaluation of 3‑carboxy‑coumarin sulfonamides as potential antiproliferative agents targeting HDAC6.
Biomed Rep
January 2025
Faculty of Chemical Sciences, University of Colima, Coquimatlán 28400, Mexico.
Breast cancer (BC) is the most common cancer and the main cause of mortality due to cancer in women around the World. Histone deacetylase 6 (HDAC6) is a promising target for the treatment of BC. In the present study, a series of novel 3-carboxy-coumarin sulfonamides, analogs of belinostat, targeting HDAC6 were designed and synthesized.
View Article and Find Full Text PDFBackground: There are 49 B alleles in the ISBT ABO blood group list. This study will describe a new missense mutation, c.784G>T, in exon 7 of the ABO in a Chinese individual.
View Article and Find Full Text PDFMicroglia depletion reduces human neuronal APOE4-related pathologies in a chimeric Alzheimer's disease model.
Cell Stem Cell
January 2025
Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Gladstone Center for Translational Advancement, Gladstone Institutes, San Francisco, CA, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA, USA. Electronic address:
Despite strong evidence supporting the important roles of both apolipoprotein E4 (APOE4) and microglia in Alzheimer's disease (AD) pathogenesis, the effects of microglia on neuronal APOE4-related AD pathogenesis remain elusive. To examine such effects, we utilized microglial depletion in a chimeric model with induced pluripotent stem cell (iPSC)-derived human neurons in mouse hippocampus. Specifically, we transplanted homozygous APOE4, isogenic APOE3, and APOE-knockout (APOE-KO) iPSC-derived human neurons into the hippocampus of human APOE3 or APOE4 knockin mice and then depleted microglia in half of the chimeric mice.
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