ResearchPad - database-update https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Biopanning data bank 2018: hugging next generation phage display]]> https://www.researchpad.co/article/elastic_article_7250 The 2018 update of the biopanning data bank (BDB) stores phage display data sequenced by Sanger sequencing and next generation sequencing technologies. In this work, we upgraded the database with more biopanning data sets and several new features, including (i) incorporation of next generation biopanning data and the unselected population where the target is not determined and the round of screening is zero; (ii) addition of sequencing information; (iii) improvement of browsing and searching systems and 3 D chemical structure viewer; (iv) integration of standalone tools for target-unrelated peptides analysis within conventional phage display and next generation phage display (NGPD) data. In the current version of BDB (released on 19 January 2018), the database houses 3291 sets of biopanning data collected from 1540 published articles, including 95 NGPD data sets and 3196 traditional biopanning data sets. The BDB database serves as an important and comprehensive resource for developing peptide ligands.

Database URL: The BDB database is available at http://immunet.cn/bdb

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<![CDATA[HTT-DB: new features and updates]]> https://www.researchpad.co/article/elastic_article_7248 Horizontal Transfer (HT) of genetic material between species is a common phenomenon among Bacteria and Archaea species and several databases are available for information retrieval and data mining. However, little attention has been given to this phenomenon among eukaryotic species mainly due to the lower proportion of these events. In the last years, a vertiginous amount of new HT events involving eukaryotic species was reported in the literature, highlighting the need of a common repository to keep the scientific community up to date and describe overall trends. Recently, we published the first HT database focused on HT of transposable elements among eukaryotes: the Horizontal Transposon Transfer DataBase: Database URL: (http://lpa.saogabriel.unipampa.edu.br: 8080/httdatabase/). Here, we present new features and updates of this unique database: (i) its expansion to include virus-host exchange of genetic material, which we called Horizontal Virus Transfer (HVT) and (ii) the availability of a web server for HT detection, where we implemented the online version of vertical and horizontal inheritance consistence analysis (VHICA), an R package developed for HT detection. These improvements will help researchers to navigate through known HVT cases, take data-informed decision and export figures based on keywords searches. Moreover, the availability of the VHICA as an online tool will make this software easily reachable even for researchers with no or little computation knowledge as well as foster our capability to detect new HT events in a wide variety of taxa.

Database URL: http://lpa.saogabriel.unipampa.edu.br:8080/httdatabase/

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<![CDATA[ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank]]> https://www.researchpad.co/article/5c5f1af8d5eed0c48469b043

Abstract

ccPDB 2.0 (http://webs.iiitd.edu.in/raghava/ccpdb) is an updated version of the manually curated database ccPDB that maintains datasets required for developing methods to predict the structure and function of proteins. The number of datasets compiled from literature increased from 45 to 141 in ccPDB 2.0. Similarly, the number of protein structures used for creating datasets also increased from ~74 000 to ~137 000 (PDB March 2018 release). ccPDB 2.0 provides the same web services and flexible tools which were present in the previous version of the database. In the updated version, links of the number of methods developed in the past few years have also been incorporated. This updated resource is built on responsive templates which is compatible with smartphones (mobile, iPhone, iPad, tablets etc.) and large screen gadgets. In summary, ccPDB 2.0 is a user-friendly web-based platform that provides comprehensive as well as updated information about datasets.

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<![CDATA[An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework]]> https://www.researchpad.co/article/5afa2665463d7e246bdb31a1

Data analysis is one of the most critical and challenging steps in drug discovery and disease biology. A user-friendly resource to visualize and analyse high-throughput data provides a powerful medium for both experimental and computational biologists to understand vastly different biological data types and obtain a concise, simplified and meaningful output for better knowledge discovery. We have previously developed TargetMine, an integrated data warehouse optimized for target prioritization. Here we describe how upgraded and newly modelled data types in TargetMine can now survey the wider biological and chemical data space, relevant to drug discovery and development. To enhance the scope of TargetMine from target prioritization to broad-based knowledge discovery, we have also developed a new auxiliary toolkit to assist with data analysis and visualization in TargetMine. This toolkit features interactive data analysis tools to query and analyse the biological data compiled within the TargetMine data warehouse. The enhanced system enables users to discover new hypotheses interactively by performing complicated searches with no programming and obtaining the results in an easy to comprehend output format.

Database URL: http://targetmine.mizuguchilab.org

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