ExPASy: SIB bioinformatics resource portal.
Panu Artimo,Manohar Jonnalagedda,Konstantin Arnold,Delphine Baratin,Gábor Csárdi,Edouard de Castro,Séverine Duvaud,Volker Flegel,Arnaud Fortier,Elisabeth Gasteiger,Aurélien Grosdidier,Céline Hernandez,Vassilios Ioannidis,Dmitry Kuznetsov,Robin Liechti,Sébastien Moretti,Khaled Mostaguir,Nicole Redaschi,Grégoire Rossier,Ioannis Xenarios,Heinz Stockinger +20 more
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TLDR
The new web interface provides, in particular, visual guidance for newcomers to ExPASy, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences.Abstract:
ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a 'decentralized' way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across 'selected' resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.read more
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The PSIPRED Protein Analysis Workbench: 20 years on.
TL;DR: The work to update the PSIPRED Protein Analysis Workbench and make it ready for the next 20 years is presented and updates to some of the key predictive algorithms available through the website are surveyed.
Journal ArticleDOI
Matrix stiffness drives epithelial–mesenchymal transition and tumour metastasis through a TWIST1–G3BP2 mechanotransduction pathway
Spencer C. Wei,Laurent Fattet,Jeff H. Tsai,Yurong Guo,Vincent Pai,Hannah E. Majeski,Albert C. Chen,Robert L. Sah,Susan S. Taylor,Adam J. Engler,Jing Yang +10 more
TL;DR: It is reported that TWIST1 is an essential mechanomediator that promotes epithelial–mesenchymal transition (EMT) in response to increasing matrix stiffness that responds to biomechanical signals from the tumour microenvironment to drive EMT, invasion and metastasis.
Journal ArticleDOI
BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA
Ida Schomburg,Antje Chang,Sandra Placzek,Carola Söhngen,Michael Rother,Maren Lang,Cornelia Munaretto,Susanne Ulas,Michael Stelzer,Andreas Grote,Maurice Scheer,Dietmar Schomburg +11 more
TL;DR: The integration of the EnzymeDetector offers an automatic comparison, evaluation and prediction of enzyme function annotations for prokaryotic genomes.
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The Cellosaurus, a Cell-Line Knowledge Resource.
TL;DR: The Cellosaurus is a key resource to help researchers identify potentially contaminated/misidentified cell lines, thus contributing to improving the quality of research in the life sciences.
Journal ArticleDOI
The Capsids of HIV-1 and HIV-2 Determine Immune Detection of the Viral cDNA by the Innate Sensor cGAS in Dendritic Cells
Xavier Lahaye,Xavier Lahaye,Takeshi Satoh,Takeshi Satoh,Matteo Gentili,Matteo Gentili,Silvia Cerboni,Silvia Cerboni,Cécile Conrad,Cécile Conrad,Ilse Hurbain,Ilse Hurbain,Ahmed El Marjou,Ahmed El Marjou,Christine Lacabaratz,Jean-Daniel Lelièvre,Nicolas Manel,Nicolas Manel +17 more
TL;DR: The HIV capsid is a determinant of innate sensing of the viral cDNA by cGAS in dendritic cells in dendedritic cells, and this pathway might potentially be harnessed to develop effective vaccines against HIV-1.
References
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ExPASy: The proteomics server for in-depth protein knowledge and analysis.
Elisabeth Gasteiger,Alexandre Gattiker,Christine Hoogland,Ivan Ivanyi,Ron D. Appel,Amos Marc Bairoch +5 more
TL;DR: The ExPASy (the Expert Protein Analysis System) World Wide Web server, provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics, provides access to a variety of databases and analytical tools dedicated to proteins and proteomics.
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A new generation of information retrieval tools for biologists: the example of the ExPASy WWW server
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The EMBRACE web service collection
Steve Pettifer,Jon Ison,Matúš Kalaš,Dave Thorne,Philip McDermott,Inge Jonassen,Ali Liaquat,José M. Fernández,Jose Manuel Rodriguez,Inb Partners,David G. Pisano,Christophe Blanchet,Mahmut Uludag,Peter Rice,Edita Bartaseviciute,Kristoffer Rapacki,Maarten L. Hekkelman,Olivier Sand,Heinz Stockinger,Andrew B. Clegg,Erik Bongcam-Rudloff,Jean Salzemann,Vincent Breton,Teresa K. Attwood,Graham Cameron,Gert Vriend +25 more
TL;DR: The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences.