Motivation
The emergence of a novel strain of betacoronavirus, SARS-CoV-2, has led to a pandemic that has been associated with over 700 000 deaths as of August 5, 2020. Research is ongoing around the ...world to create vaccines and therapies to minimize rates of disease spread and mortality. Crucial to these efforts are molecular characterizations of neutralizing antibodies to SARS-CoV-2. Such antibodies would be valuable for measuring vaccine efficacy, diagnosing exposure and developing effective biotherapeutics. Here, we describe our new database, CoV-AbDab, which already contains data on over 1400 published/patented antibodies and nanobodies known to bind to at least one betacoronavirus. This database is the first consolidation of antibodies known to bind SARS-CoV-2 as well as other betacoronaviruses such as SARS-CoV-1 and MERS-CoV. It contains relevant metadata including evidence of cross-neutralization, antibody/nanobody origin, full variable domain sequence (where available) and germline assignments, epitope region, links to relevant PDB entries, homology models and source literature.
Results
On August 5, 2020, CoV-AbDab referenced sequence information on 1402 anti-coronavirus antibodies and nanobodies, spanning 66 papers and 21 patents. Of these, 1131 bind to SARS-CoV-2.
Availabilityand implementation
CoV-AbDab is free to access and download without registration at http://opig.stats.ox.ac.uk/webapps/coronavirus. Community submissions are encouraged.
Supplementary information
Supplementary data are available at Bioinformatics online.
Too much to know Blair, Ann
2010, 20101130, 2010-11-02, 20100101
eBook, Book
The flood of information brought to us by advancing technology is often accompanied by a distressing sense of "information overload," yet this experience is not unique to modern times. In fact, says ...Ann M. Blair in this intriguing book, the invention of the printing press and the ensuing abundance of books provoked sixteenth- and seventeenth-century European scholars to register complaints very similar to our own. Blair examines methods of information management in ancient and medieval Europe as well as the Islamic world and China, then focuses particular attention on the organization, composition, and reception of Latin reference books in print in early modern Europe. She explores in detail the sophisticated and sometimes idiosyncratic techniques that scholars and readers developed in an era of new technology and exploding information.
Abstract Summary One of the first steps in single-cell omics data analysis is visualization, which allows researchers to see how well-separated cell-types are from each other. When visualizing ...multiple datasets at once, data integration/batch correction methods are used to merge the datasets. While needed for downstream analyses, these methods modify features space (e.g. gene expression)/PCA space in order to mix cell-types between batches as well as possible. This obscures sample-specific features and breaks down local embedding structures that can be seen when a sample is embedded alone. Therefore, in order to improve in visual comparisons between large numbers of samples (e.g. multiple patients, omic modalities, different time points), we introduce Compound-SNE, which performs what we term a soft alignment of samples in embedding space. We show that Compound-SNE is able to align cell-types in embedding space across samples, while preserving local embedding structures from when samples are embedded independently. Availability and implementation Python code for Compound-SNE is available for download at https://github.com/HaghverdiLab/Compound-SNE.
Abstract Summary Analysing protein structure similarities is an important step in protein engineering and drug discovery. Methodologies that are more advanced than simple RMSD are available but often ...require extensive mathematical or computational knowledge for implementation. Grouping and optimizing such tools in an efficient open-source library increases accessibility and encourages the adoption of more advanced metrics. Melodia is a Python library with a complete set of components devised for describing, comparing and analysing the shape of protein structures using differential geometry of 3D curves and knot theory. It can generate robust geometric descriptors for thousands of shapes in just a few minutes. Those descriptors are more sensitive to structural feature variation than RMSD deviation. Melodia also incorporates sequence structural annotation and 3D visualizations. Availability and implementation Melodia is an open-source Python library freely available on https://github.com/rwmontalvao/Melodia_py, along with interactive Jupyter Notebook tutorials.
Abstract Motivation The post-processing and analysis of large-scale untargeted metabolomics data face significant challenges due to the intricate nature of correction, filtration, imputation, and ...normalization steps. Manual execution across various applications often leads to inefficiencies, human-induced errors, and inconsistencies within the workflow. Results Addressing these issues, we introduce MetaboLink, a novel web application designed to process LC-MS metabolomics datasets combining established methodologies and offering flexibility and ease of implementation. It offers visualization options for data interpretation, an interface for statistical testing, and integration with PolySTest for further tests and with VSClust for clustering analysis. Availability and implementation Fully functional tool is publicly available at https://computproteomics.bmb.sdu.dk/Metabolomics/. The source code is available at https://github.com/anitamnd/MetaboLink and a detailed description of the app can be found at https://github.com/anitamnd/MetaboLink/wiki. A tutorial video can be found at https://youtu.be/ZM6j10S6Z8Q.
Abstract Summary perox-per-cell automates cumbersome, image-based data collection tasks often encountered in peroxisome research. The software processes microscopy images to quantify peroxisome ...features in yeast cells. It uses off-the-shelf image processing tools to automatically segment cells and peroxisomes and then outputs quantitative metrics including peroxisome counts per cell and spatial areas. In validation tests, we found that perox-per-cell output agrees well with manually quantified peroxisomal counts and cell instances, thereby enabling high-throughput quantification of peroxisomal characteristics. Availability and implementation The software is coded in Python. Compiled executables and source code are available at https://github.com/AitchisonLab/perox-per-cell.
Abstract Summary Identification and quantification of phosphorylation sites are essential for biological interpretation of a phosphoproteomics experiment. For data independent acquisition mass ...spectrometry-based (DIA-MS) phosphoproteomics, extracting a site-level report from the output of current processing software is not straightforward as multiple peptides might contribute to a single site, multiple phosphorylation sites can occur on the same peptides, and protein isoforms complicate site specification. Currently only limited support is available from a commercial software package via a platform-specific solution with a rather simple site quantification method. Here, we present sitereport, a software tool implemented in an extendable Python package called msproteomics to report phosphosites and phosphopeptides from a DIA-MS phosphoproteomics experiment with a proven quantification method called MaxLFQ. We demonstrate the use of sitereport for downstream data analysis at site level, allowing benchmarking different DIA-MS processing software tools. Availability and implementation sitereport is available as a command line tool in the Python package msproteomics, released under the Apache License 2.0 and available from the Python Package Index (PyPI) at https://pypi.org/project/msproteomics and GitHub at https://github.com/tvpham/msproteomics.
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