Abstract
Due to the increasing amount of publicly available protein structures searching, enriching and investigating these data still poses a challenging task. The ProteinsPlus web service ...(https://proteins.plus) offers a broad range of tools addressing these challenges. The web interface to the tool collection focusing on protein–ligand interactions has been geared towards easy and intuitive access to a large variety of functionality for life scientists. Since our last publication, the ProteinsPlus web service has been extended by additional services as well as it has undergone substantial infrastructural improvements. A keyword search functionality was added on the start page of ProteinsPlus enabling users to work on structures without knowing their PDB code. The tool collection has been augmented by three tools: StructureProfiler validates ligands and active sites using selection criteria of well-established protein–ligand benchmark data sets, WarPP places water molecules in the ligand binding sites of a protein, and METALizer calculates, predicts and scores coordination geometries of metal ions based on surrounding complex atoms. Additionally, all tools provided by ProteinsPlus are available through a REST service enabling the automated integration in structure processing and modeling pipelines.
The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. The ...current version introduces four new dataset types, together with numerous new features. Annotation options have been expanded and new control options added for many display elements. An interactive spreadsheet-like editor has been implemented, providing dataset creation and editing directly in the web interface. Font support has been rewritten with full support for UTF-8 character encoding throughout the user interface. Google Web Fonts are now fully supported in the tree text labels. iTOL v4 is the first tool which supports direct visualization of Qiime 2 trees and associated annotations. The user account system has been streamlined and expanded with new navigation options, and currently handles >700 000 trees from more than 40 000 individual users. Full batch access has been implemented allowing programmatic upload and export of trees and annotations.
Abstract
Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are ...now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.
AN OPEN SOURCE MAIL SERVER MIGRATION EXPERIENCE: IREDMAIL Azginoglu, N.
International archives of the photogrammetry, remote sensing and spatial information sciences.,
11/2020, Volume:
XLIV-4/W3-2020
Journal Article, Conference Proceeding
Peer reviewed
Open access
Servers are systems that set up to run for years, but it may be necessary to migrate to a new, better server when they have completed their lifetime or become inadequate. In this study, the ...open-source iRedMail e-mail server has been successfully migrated to another high-capacity physical server which uses an open-source CentOS operation system. Migration is a process that every step has to be very well planned. However, although planning is well done, unexpected errors may occur. For this reason, it is also essential to choose migration time. The experience gained as a result of the study is a guide for the new ones.
WebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers and 155 175 ...functional categories, as well as user-uploaded functional databases. To address the growing and unique need for phosphoproteomics data interpretation, we have implemented phosphosite set analysis to identify important kinases from phosphoproteomics data. We have completely redesigned result visualizations and user interfaces to improve user-friendliness and to provide multiple types of interactive and publication-ready figures. To facilitate comprehension of the enrichment results, we have implemented two methods to reduce redundancy between enriched gene sets. We introduced a web API for other applications to get data programmatically from the WebGestalt server or pass data to WebGestalt for analysis. We also wrapped the core computation into an R package called WebGestaltR for users to perform analysis locally or in third party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org.
Botnets are one of the leading threats to network security nowadays and are used to conduct a wide variety of malicious activities, including information theft, phishing, spam mail distribution, and ...Distributed Denial of Service (DDoS) attacks. Among the various forms of botnet, DGA-based botnets, which utilize a Domain Generation Algorithm (DGA) to avoid detection, are one of the most disruptive and difficult to detect. In such botnets, the DGA is used to generate a huge list of candidate Command and Control (C&C) server domains, and the bot then attempts to connect to an active C&C server by querying each DNS server in turn. DGA-based botnets are highly elusive and difficult to detect using traditional defensive mechanisms and therefore have a high survivability. Accordingly, this study proposes a DGA-based botnet detection scheme designated as DBod based on an analysis of the query behavior of the DNS traffic. The proposed scheme exploits the fact that hosts compromised by the same DGA-based malware query the same sets of domains in the domain list and most of these queries fail since only a very limited number of the domains are actually associated with an active C&C. The feasibility of the proposed method is evaluated using the DNS data collected from an education network environment over a period of 26 months. The results show that DBod provides an accurate and effective means of detecting both existing and new DGA-based botnet patterns in real-world networks.
How good is automated protein docking? Kozakov, Dima; Beglov, Dmitri; Bohnuud, Tanggis ...
Proteins, structure, function, and bioinformatics,
December 2013, Volume:
81, Issue:
12
Journal Article
The rapid increase in user base and technological penetration has enabled the use of a wide range of devices and applications. The services are rendered to these devices from single-server or highly ...distributed server environments, irrespective of their location. As the information exchanged between servers and clients is private, numerous forms of attacks can be launched to compromise it. To ensure the security, privacy, and availability of the services, different authentication schemes have been proposed for both single-server and multi-server environments. The primary performance objective of such schemes is to prevent most (if not all) attacks, with minimal computational costs at the server and user ends. To address this challenge, this paper presents a secure user authentication scheme with anonymity (SUAA) for single-server and multi-server environments. It works on 3-factor authentication, involving passwords, smart cards, and biometric data. We use symmetric and asymmetric encryption for single-server and multi-server architectures respectively, to reduce the computational costs. Through a comprehensive security analysis, we show that the proposed scheme is reliable through mutual authentication, and is resilient to attacks addressed by state of the art solutions. Time cost analysis also shows less time required to complete the authentication process.
Microbial natural products represent a rich resource of pharmaceutically and industrially important compounds. Genome sequencing has revealed that the majority of natural products remain ...undiscovered, and computational methods to connect biosynthetic gene clusters to their corresponding natural products therefore have the potential to revitalize natural product discovery. Previously, we described PRediction Informatics for Secondary Metabolomes (PRISM), a combinatorial approach to chemical structure prediction for genetically encoded nonribosomal peptides and type I and II polyketides. Here, we present a ground-up rewrite of the PRISM structure prediction algorithm to derive prediction of natural products arising from non-modular biosynthetic paradigms. Within this new version, PRISM 3, natural product scaffolds are modeled as chemical graphs, permitting structure prediction for aminocoumarins, antimetabolites, bisindoles and phosphonate natural products, and building upon the addition of ribosomally synthesized and post-translationally modified peptides. Further, with the addition of cluster detection for 11 new cluster types, PRISM 3 expands to detect 22 distinct natural product cluster types. Other major modifications to PRISM include improved sequence input and ORF detection, user-friendliness and output. Distribution of PRISM 3 over a 300-core server grid improves the speed and capacity of the web application. PRISM 3 is available at http://magarveylab.ca/prism/.
Abstract
SNPnexus is a web-based annotation tool for the analysis and interpretation of both known and novel sequencing variations. Since its last release, SNPnexus has received continual updates to ...expand the range and depth of annotations provided. SNPnexus has undergone a complete overhaul of the underlying infrastructure to accommodate faster computational times. The scope for data annotation has been substantially expanded to enhance biological interpretations of queried variants. This includes the addition of pathway analysis for the identification of enriched biological pathways and molecular processes. We have further expanded the range of user directed annotation fields available for the study of cancer sequencing data. These new additions facilitate investigations into cancer driver variants and targetable molecular alterations within input datasets. New user directed filtering options have been coupled with the addition of interactive graphical and visualization tools. These improvements streamline the analysis of variants derived from large sequencing datasets for the identification of biologically and clinically significant subsets in the data. SNPnexus is the most comprehensible web-based application currently available and these new set of updates ensures that it remains a state-of-the-art tool for researchers. SNPnexus is freely available at https://www.snp-nexus.org.
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