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Egon Willighagen › Comments

Egon Willighagen
MicroRNA modulation of lipid metabolism and oxidative stress in cardiometabolic diseases - http://www.citeulike.org/user...
Free Radical Biology and Medicine, Vol. 64 (September 2013), pp. 31-39, doi:10.1016/j.freeradbiomed.2013.07.014 Juan Aranda, Julio Madrigal-Matute, Noemi Rotllan, Carlos Fernández-Hernando - Egon Willighagen
Egon Willighagen
On the formulation of performant SPARQL queries - http://www.citeulike.org/user...
Web Semantics: Science, Services and Agents on the World Wide Web (November 2014), doi:10.1016/j.websem.2014.11.003 Antonis Loizou, Renzo Angles, Paul Groth - Egon Willighagen
Egon Willighagen
Drug discovery FAQs: workflows for answering multidomain drug discovery questions - http://www.citeulike.org/user...
Drug Discovery Today (November 2014), doi:10.1016/j.drudis.2014.11.006 Christine Chichester, Daniela Digles, Ronald Siebes, Antonis Loizou, Paul Groth, Lee Harland - Egon Willighagen
Egon Willighagen
Impacts of Nanoparticles on Cardiovascular Diseases: Modulating Metabolism and Function of Endothelial Cells - http://www.citeulike.org/user...
Current Drug Metabolism, Vol. 13, No. 8. (01 September 2012), pp. 1123-1129, doi:10.2174/138920012802850056 Jie Meng, Xian-da Yang, Lee Jia, Xing-Jie Liang, Chen Wang - Egon Willighagen
Egon Willighagen
Tonight on Dutch national TV. - https://plus.google.com/1041867...
Tonight on Dutch national TV. The Internet's Own Boy: The Story of Aaron Swartz ( (2014)) met Tim Berners-Lee, Cindy Cohn, Gabriella Coleman. Regie: Brian Knappenberger. Het verhaal van programmeur en informatie-activist Aaron Schwartz, die op 26-jarige leeftijd zelfmoord pleegde. .. - Egon Willighagen
Egon Willighagen
The parallel worlds of public and commercial bioactive chemistry data. - http://www.citeulike.org/user...
Journal of medicinal chemistry (21 November 2014) The availability of structures and linked bioactivity data in databases is powerfully enabling for drug discovery and chemical biology. However, we now review some confounding issues with the divergent expansions of public and commercial sources of chemical structures. These are not only associated with expanding patent extraction but also increasingly large vendor collections amassed via different selection criteria between the Chemical Abstracts Service (CAS) SciFinder® and major public sources such as PubChem, ChemSpider, UniChem and others. These increasingly massive collections may include both real and virtual compounds, as well as so-called prophetic compounds from patents. We address a range of issues raised by the challenges faced resolving the NIH probe compounds. In addition we highlight the confounding of prior-art searching by virtual compounds which could impact the composition of matter patentability of a new medicinal... - Egon Willighagen
Egon Willighagen
Reshared post from Matthew Todd: - https://plus.google.com/1041867...
Original Post from Matthew Todd: Gah - more on Chemdraw solubility prediction via LogP and CLogP - obviously depends on which tautomer you draw, but also depends on those explicit/implicit H's on heteroatoms. (Shortcut directly to relevant picture in post: http://malaria.ourexperiment.org/data...) Anyone know to what extent we ought to worry? We're using a predicted logP threshold of about 3. Obviously if we are wrongly calculating logP then we could be designing analogs wrongly. Should we switch to some other resource as standard (ideally one open to the whole community)? Solubility is becoming an increasingly crucial aspect of design in OSM Series 4, and a major outcome of the latest meeting. OSM Online Project Meeting 9 (24th Nov 2014). was to ensure that all compounds being made have a healthy predicted logP value of below 3.5 or so. - Egon Willighagen
Egon Willighagen
BridgeDb: BridgeDb 2.0.0 released - http://www.citeulike.org/user...
ZENODO (24 November 2014), doi:10.5281/zenodo.12839 CY Brenninkmeijer, E Willighagen, A Pico, M Summer-Kutmon - Egon Willighagen
Egon Willighagen
Reshared post from Jan Jensen: - https://plus.google.com/1041867...
Original Post from Jan Jensen: Computing a accessible surface area using Jmol Someone asked me how to compute a surface area of a molecule.  Here's how to compute a solvent accessible surface area using Jmol . 1. Load your molecule into Jmol (File > Open) 2. Open the Script Editor and Output Console (File > Script Editor, etc) 3. Typ... Someone asked me how to compute a surface area of a molecule. Here's how to compute a solvent accessible surface area using Jmol. 1. Load your molecule into Jmol (File > Open) 2. Open the Script Editor and Output Console (File > Script Editor, etc) 3. Type the following three lines into the ... - Egon Willighagen
Egon Willighagen
Powered by Linked Data. Only in English at this moment, it seems. Playable with ChromeCast and one or... - https://plus.google.com/1041867...
Powered by Linked Data. Only in English at this moment, it seems. Playable with ChromeCast and one or more phone/tablets behind your TV. Includes science questions. Enjoyable! - Egon Willighagen
Egon Willighagen
Egon Willighagen
Yesterday I started the Computational Chemistry Daily which aggregates posts related to computational chemistry on social media such as Twitter, Google+ and Facebook on a daily basis. It identifies the posts by certain words or hashtags such as #compchem and everyone can contribute. - Egon Willighagen
Egon Willighagen
Inroads to Predict in Vivo Toxicology—An Introduction to the eTOX Project - http://www.citeulike.org/user...
International Journal of Molecular Sciences, Vol. 13, No. 3. (21 March 2012), pp. 3820-3846, doi:10.3390/ijms13033820 There is a widespread awareness that the wealth of preclinical toxicity data that the pharmaceutical industry has generated in recent decades is not exploited as efficiently as it could be. Enhanced data availability for compound comparison (“read-across”), or for data mining to build predictive tools, should lead to a more efficient drug development process and contribute to the reduction of animal use (3Rs principle). In order to achieve these goals, a consortium approach, grouping numbers of relevant partners, is required. The eTOX (“electronic toxicity”) consortium represents such a project and is a public-private partnership within the framework of the European Innovative Medicines Initiative (IMI). The project aims at the development of in silico prediction systems for organ and in vivo toxicity. The backbone of the project will be a database consisting of... - Egon Willighagen
Egon Willighagen
The eTOX Data-Sharing Project to Advance in Silico Drug-Induced Toxicity Prediction - http://www.citeulike.org/user...
International Journal of Molecular Sciences, Vol. 15, No. 11. (14 November 2014), pp. 21136-21154, doi:10.3390/ijms151121136 The high-quality in vivo preclinical safety data produced by the pharmaceutical industry during drug development, which follows numerous strict guidelines, are mostly not available in the public domain. These safety data are sometimes published as a condensed summary for the few compounds that reach the market, but the majority of studies are never made public and are often difficult to access in an automated way, even sometimes within the owning company itself. It is evident from many academic and industrial examples, that useful data mining and model development requires large and representative data sets and careful curation of the collected data. In 2010, under the auspices of the Innovative Medicines Initiative, the eTOX project started with the objective of extracting and sharing preclinical study data from paper or pdf archives of toxicology departments... - Egon Willighagen
Egon Willighagen
Reshared post from Susanna-Assunta Sansone: - https://plus.google.com/1041867...
Original Post from Susanna-Assunta Sansone: Editorial and News: Nature and the Nature research journals are strengthening their editorial links with Scientific Data to enhance their data-availability practices! With our ISA and BioSharing work  - supporting Scientific Data - we are very glad to be part of and help with this process. Data-access practices strengthened - Egon Willighagen
Egon Willighagen
A network biology workflow to study transcriptomics data of the diabetic liver - http://www.citeulike.org/user...
BMC Genomics, Vol. 15, No. 1. (15 November 2014), 971, doi:10.1186/1471-2164-15-971 BACKGROUND:Nowadays a broad collection of transcriptomics data is publicly available in online repositories. Methods for analyzing these data often aim at deciphering the influence of gene expression at the process level. Biological pathway diagrams depict known processes and capture the interactions of gene products and metabolites, information that is essential for the computational analysis and interpretation of transcriptomics data. The present study describes a comprehensive network biology workflow that integrates differential gene expression in the human diabetic liver with pathway information by building a network of interconnected pathways. Worldwide, the incidence of type 2 diabetes mellitus is increasing dramatically, and to better understand this multifactorial disease, more insight into the concerted action of the disease-related processes is needed. The liver is a key player in metabolic... - Egon Willighagen
Egon Willighagen
Defining Molecular Initiating Events in the Adverse Outcome Pathway Framework for Risk Assessment - http://www.citeulike.org/user...
Chem. Res. Toxicol. (29 October 2014), doi:10.1021/tx500345j Consumer and environmental safety decisions are based on exposure and hazard data, interpreted using risk assessment approaches. The adverse outcome pathway (AOP) conceptual framework has been presented as a logical sequence of events or processes within biological systems which can be used to understand adverse effects and refine current risk assessment practices in ecotoxicology. This framework can also be applied to human toxicology and is explored on the basis of investigating the molecular initiating events (MIEs) of compounds. The precise definition of the MIE has yet to reach general acceptance. In this work we present a unified MIE definition: an MIE is the initial interaction between a molecule and a biomolecule or biosystem that can be causally linked to an outcome via a pathway. Case studies are presented, and issues with current definitions are addressed. With the development of a unified MIE definition, the... - Egon Willighagen
Egon Willighagen
Scientists report a new method for establishing whether chemical compounds are safe for human use without "in vivo" testing, based on so-called "molecular initiating events" at the boundary between chemistry and biology. - Egon Willighagen
Egon Willighagen
Congratulations to Pekka and Roland for their important work on alternatives for animal testing! (HT... - https://plus.google.com/1041867...
Congratulations to Pekka and Roland for their important work on alternatives for animal testing! (HT to Barry for the pointer) We are delighted to announce 12 outstanding winners of the 2014 Lush Prize Awards, sharing £250,00 in prize money. - Egon Willighagen
Egon Willighagen
Reshared post from John May: - https://plus.google.com/1041867...
Original Post from John May: Some fun with Scala's implicit methods, CDK, and RDKit. Earlier this year I wrote up some Chemical Toolkit Rosetta examples of using the CDK in Scala (github/cdk/cdk-scala-examples). When I was writing this it sprung to mind that it would be cool to (ab)use one feature for interop... - Egon Willighagen
Egon Willighagen
Programming in the Life Sciences #20: extracting data from JSON I previously wrote about the JavaScript... - https://plus.google.com/1041867...
Programming in the Life Sciences #20: extracting data from JSON I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because of its clear link to ontologies,... I previously wrote about the JavaScript Object Notation (JSON) which has become a de facto standard for sharing data by web services. I personally still prefer something using the Resource Description Framework (RDF) because ... - Egon Willighagen
Egon Willighagen
Programming in the Life Sciences #19: debugging Debugging is the process find removing a fault in your... - https://plus.google.com/1041867...
Programming in the Life Sciences #19: debugging Debugging is the process find removing a fault in your code ( the etymology goes further back than the moth story, I learned today). Being able to debug is an essential programming skill, and being able to program flawlessly is not enough; the bug can be ou... Debugging is the process find removing a fault in your code (the etymology goes further back than the moth story, I learned today). Being able to debug is an essential programming skill, and being able to program flawlessly i... - Egon Willighagen
Egon Willighagen
BioScience, Vol. 63, No. 4. (1 April 2013), pp. 245-246, doi:10.1525/bio.2013.63.4.2 Paula Stephan - Egon Willighagen
Egon Willighagen
We are continuing with our weekly releases of highly-requested items from the ORCID iDeas Forum. This post includes the third end-of-the-year goody that we recently released: ORCID iD QR codes. You can now get a scannable QR Code that points to your ORCID iD. In addition, we’ve teamed up with Zazzle.com to format the QR code to be printed on stickers that you can add to your posters and other presentation materials. - Egon Willighagen
Egon Willighagen
Mmm... buffer I don't know yet... - https://plus.google.com/1041867...
Mmm... buffer I don't know yet...  We explore Buffer, Hootsuite, and IFTTT to help academics find the best ways to save time managing their social media accounts. - Egon Willighagen
Egon Willighagen
One hour HTML+ops.js+d3.js hack! I love good libraries! - Egon Willighagen
Egon Willighagen
Honorary degrees will be awarded during the official celebration of the Dies Natalis on 16 January 2015 - Egon Willighagen
Egon Willighagen
Reshared post from PHD Comics: - https://plus.google.com/1041867...
And then people wonder why the retraction rate is going up :) Original Post from PHD Comics: The academic review process. http://www.phdcomics.com/comics... Link to Piled Higher and Deeper - Egon Willighagen
Egon Willighagen
Maastricht railway station - http://en.wikipedia.org/w...
Egonw: {{Infobox station | name = Maastricht | style = NS | image = Maastricht, station.gif | image_caption = | address = | country = [[Netherlands]] | latd = 50|latm = 51|lats = 00 |latNS = N | longd = 5|longm = 42|longs = 19 |longEW = E | iso_region = NL | coordinates_display = yes | line = [[Maastricht–Venlo railway]]<br>[[Maastricht–Aachen railway]]<br>[[Liège–Maastricht railway]] | platform = | opened = 1853 | closed = | code = | services = {{s-rail|title=Nederlandse Spoorwegen}} {{s-line|system=NS Intercity|line=800|branch=800|previous=Sittard|next=}} {{s-line|system=NS Sneltrein|line=32100|previous=|next=Meerssen}} {{s-line|system=NS Stoptrein|line=5300|previous=|next=Maastricht Randwyck}} {{s-line|system=NS Stoptrein|line=6800|previous=Bunde|next=Maastricht Randwyck}} {{s-line|system=NS Stoptrein|line=32000|previous=Maastricht Randwyck|next=Maastricht Noord}} | map_type = Netherlands Dutch railway station | map_caption = }} '''Maastricht''' is a [[railway station]] located in... - Egon Willighagen
Egon Willighagen
Interaction between DNA/histone Methyltransferases and their Inhibitors. - http://www.citeulike.org/user...
Current medicinal chemistry (5 November 2014) Epigenetic research has recently become one of the hotspots in the field of bioscience and drug design. DNA methylation and histone methylation serve a critical function in influencing gene expression and genome function. The inhibition of DNA and histone methyltransferases (DNMTs and HMTs) is a promising approach for the therapeutic treatment of numerous diseases, including cancer. This work reviews the recent achievements in methyltransferase crystallographic structure resolution and bioactive inhibitor screening. We discuss the features of DNA and HMT structures, as well as the mechanism and structure-function relationship of transferase inhibitors, to elucidate how methyltransferase and inhibitor interactions occur both internally and externally. This study briefly reviews the biological function, as well as the inhibitor discovery and development, of DNA/histone methyltransferases. Junchi Hu, Shijie Chen, Xiangqian Kong, Kongkai Zhu,... - Egon Willighagen
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