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Egon Willighagen › Comments

Egon Willighagen
Original Post from Fon: This is how The Netherlands looks after the roll out of our joint network started. Amazing huh? There are lots of Fon Spots to connect to wherever you go! http://bit.ly/FonMaps Screen Shot 2014-07-16 at 10.05.49.png - Egon Willighagen
Egon Willighagen
Egonw: Updated the link out to the Blue Obelisk wiki, as SourceForge changed their set up. {{Infobox organization |name = Blue Obelisk |image = BOicon.png |image_border = |size = 50px |alt = |caption = |map = |msize = |malt = |mcaption = |abbreviation = |motto = |formation = 2005 |extinction = |type = |status = |purpose = |headquarters = |location = |region_served = |membership = 23+ |language = English |leader_title = |leader_name = |main_organ = |parent_organization = |affiliations = |num_staff = |num_volunteers = |budget = zero |website = http://www.blueobelisk.org/ |remarks = }} '''Blue Obelisk''' is an informal group of chemists who promote [[open data]], [[open source]], and [[open standards]]; it was initiated by [[Peter Murray-Rust]] and others in 2005.<ref>P. Murray-Rust, The Blue Obelisk, [[Chemistry Development Kit#CDK News|CDK News]], 2005, 2, 43&ndash;46</ref><ref>{{cite journal | last1 = Guha | first1 = R | last2 = Howard | first2 = MT | last3 = Hutchison | first3 = GR |... - Egon Willighagen
Egon Willighagen
Egonw: {{Infobox organization |name = Blue Obelisk |image = BOicon.png |image_border = |size = 50px |alt = |caption = |map = |msize = |malt = |mcaption = |abbreviation = |motto = |formation = 2005 |extinction = |type = |status = |purpose = |headquarters = |location = |region_served = |membership = 23+ |language = English |leader_title = |leader_name = |main_organ = |parent_organization = |affiliations = |num_staff = |num_volunteers = |budget = zero |website = http://www.blueobelisk.org/ |remarks = }} '''Blue Obelisk''' is an informal group of chemists who promote [[open data]], [[open source]], and [[open standards]]; it was initiated by [[Peter Murray-Rust]] and others in 2005.<ref>P. Murray-Rust, The Blue Obelisk, [[Chemistry Development Kit#CDK News|CDK News]], 2005, 2, 43&ndash;46</ref><ref>{{cite journal | last1 = Guha | first1 = R | last2 = Howard | first2 = MT | last3 = Hutchison | first3 = GR | last4 = Murray-Rust | first4 = P | last5 = Rzepa | first5 = H | last6 = Steinbeck |... - Egon Willighagen
Egon Willighagen
Original Post from Toxtree: Toxtree protein binding alerts  http://toxtree.sourceforge.net/protein... used in  Van der, J. W., Soeteman-Hernández, L. G., Ezendam, J., Stierum, R., Kuper, F. C., & van Loveren, H. (2014). Anchoring molecular mechanisms to the adverse outcome pathway for skin sensitization: Analysis of existing data. Critical Reviews in Toxicology, 1–10. http://www.ncbi.nlm.nih.gov/pubmed... Home. Toxtree. Download. Toxtree 2.6.6 · Toxtree 2.6.0 · Toxtree 2.5.4 · Toxtree 2.5.1 · Toxtree 2.5.0 · Toxtree 2.2.0 · Toxtree 2.1.0 · Toxtree 1.60 · Toxtree 1.51 · Toxtree 1.20. Plugins. Cramer rules · Extended Cramer rules · Verhaar scheme · Modified Verhaar scheme · Skin irritation ... - Egon Willighagen
Egon Willighagen
Scary... "Timeghost" http://feedly.com/e/ipDfWJSF < Prev · Random; Next >; >|. Permanent link to this comic: http://xkcd.com/1393/ Image URL (for hotlinking/embedding): http://imgs.xkcd.com/comics.... Selected Comics. Search comic titles and transcripts: RSS Feed - Atom Feed. Comics I enjoy: Three Word Phrase, Oglaf (nsfw), SMBC, ... - Egon Willighagen
Egon Willighagen
Fingerprint Searching Using Various Indexing Methods - Egon Willighagen
Egon Willighagen
Reshared post from Truthloader: - https://plus.google.com/1041867...
Of course, what we want is an interactive version, not an animated GIF... in fact, we want this in Google Maps... Original Post from Truthloader: I know you've all been waiting for it... so here it is #GIFTUESDAY    (on Wednesday) Unbelievable bit of footage from the ISS of this volcano erupting, BUT WAIT THERE'S MORE... For more International Space Station shenanigans, if you haven't heard of astronaut Chris Hadfield, he's pretty cool. Here's what he has done: Why astronaut Chris Hadfield is a legend - Truthloader #iss   #space   #volcano   volcano.gif - Egon Willighagen
Egon Willighagen
Reshared post from Jan Jensen: - https://plus.google.com/1041867...
Interesting! I see no reason to still implement HF in Fortran...  Original Post from Jan Jensen: Overview¶. PyQuante (Sourceforge Project Page) is an open-source suite of programs for developing quantum chemistry methods. The program is written in the Python programming language, but has many “rate-determining” modules also written in C for speed. The resulting code, though not as fast as ... - Egon Willighagen
Egon Willighagen
Chimpanzee Intelligence Is Heritable - http://www.citeulike.org/user...
Current Biology (July 2014), doi:10.1016/j.cub.2014.05.076 William Hopkins, Jamie Russell, Jennifer Schaeffer - Egon Willighagen
Egon Willighagen
Dutch civilian rights organization calls for massive adoption for Tor and encryption in general, as ... - https://plus.google.com/1041867...
Dutch civilian rights organization calls for massive adoption for Tor and encryption in general, as reaction to new leaks showing NSA thinks anyone who cares about civilian rights is a potential "extremist". Geef de NSA meer uien om te pellen - Egon Willighagen
Egon Willighagen
Electrical stimulation of a small brain area reversibly disrupts consciousness - http://www.citeulike.org/user...
Epilepsy &#38; Behavior, Vol. 37 (August 2014), pp. 32-35, doi:10.1016/j.yebeh.2014.05.027 Mohamad Koubeissi, Fabrice Bartolomei, Abdelrahman Beltagy, Fabienne Picard - Egon Willighagen
Egon Willighagen
Reshared post from Vedrin Jeliazkov: - https://plus.google.com/1041867...
Useful for all your research under EC-funded project NDAs.... Original Post from Vedrin Jeliazkov: This service could make big waves in the webmail swamp. Secure email with absolutely no compromises, brought to you by MIT and CERN scientists. Follow us for live updates. - Egon Willighagen
Egon Willighagen
#JChemInf Volume 5 as PDF on @FigShare One of the things I do to prepare for holiday, is get some reading... - https://plus.google.com/1041867...
#JChemInf Volume 5 as PDF on @FigShare One of the things I do to prepare for holiday, is get some reading stuff together. I haven't finished Gödel, Escher, Bach yet (a suggested from the blogosphere), with a bit of luck there are new chapters of HPMOR , and I normally try to catch up with litera... One of the things I do to prepare for holiday, is get some reading stuff together. I haven't finished Gödel, Escher, Bach yet (a suggested from the blogosphere), with a bit of luck there are new chapters of HPMOR, and I norma... - Egon Willighagen
Egon Willighagen
Reshared post from Joerg Fliege: - https://plus.google.com/1041867...
We must never forget that wars normally do not end because the opponent was convinced about your argument, but because the number of soldiers and civilians left ran out... Original Post from Joerg Fliege: The First World War, in new pictures Headline chosen with care, as some of the pictures displayed have only recently been digitized,  and the curator has trawled extensive collections of the war to find and display photographs that have not been shown on mass media before. So, 'new' in this sense. A poignant, well-chosen display, executed with great care. The full collection is available at http://www.theatlantic.com/static... and subdivided into 10 subsections. The picture here shows Royal Army Medical Corps men, searching the packs of the British dead for letters and effects to be sent to relatives after the Battle of Guillemont, Somme, France, September of 1916. w_32.jpg - Egon Willighagen
Egon Willighagen
Investigating the contribution of CYP2J2 to ritonavir metabolism in vitro and in vivo - http://www.citeulike.org/user...
Biochemical Pharmacology (June 2014), doi:10.1016/j.bcp.2014.06.020 Rüdiger Kaspera, Brian Kirby, Tariku Sahele, Ann Collier, Evan Kharasch, Jashvant Unadkat, Rheem Totah - Egon Willighagen
Egon Willighagen
The human circadian metabolome - http://www.citeulike.org/user...
Proceedings of the National Academy of Sciences, Vol. 109, No. 7. (14 February 2012), pp. 2625-2629, doi:10.1073/pnas.1114410109 The circadian clock orchestrates many aspects of human physiology, and disruption of this clock has been implicated in various pathologies, ranging from cancer to metabolic syndrome and diabetes. Although there is evidence that metabolism and the circadian clockwork are intimately linked on a transcriptional level, whether these effects are directly under clock control or are mediated by the rest–activity cycle and the timing of food intake is unclear. To answer this question, we conducted an unbiased screen in human subjects of the metabolome of blood plasma and saliva at different times of day. To minimize indirect effects, subjects were kept in a 40-h constant routine of enforced posture, constant dim light, hourly isocaloric meals, and sleep deprivation. Under these conditions, we found that ∼15% of all identified metabolites in plasma and saliva were... - Egon Willighagen
Egon Willighagen
Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds. - http://www.citeulike.org/user...
Journal of cheminformatics, Vol. 1, No. 1. (2009), 10, doi:10.1186/1758-2946-1-10 Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel, commercial sources that extract and curate such relationships from journals and patents have also been expanding. This work updates a previous comparative study of databases chosen because of their bioactive content, availability of downloads and facility to select informative subsets. Where they could be calculated, extracted compounds-per-journal article were in the range of 12 to 19 but compound-per-protein counts increased with document numbers. Chemical structure filtration to facilitate standardised comparisons typically reduced source counts by between 5% and 30%. The pair-wise overlaps between 23 databases and subsets were determined, as well as changes between 2006 and 2008. While all... - Egon Willighagen
Egon Willighagen
Comparing the Chemical Structure and Protein Content of ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database. - http://www.citeulike.org/user...
Molecular informatics, Vol. 32, No. 11-12. (December 2013), pp. 881-897 ChEMBL, DrugBank, Human Metabolome Database and the Therapeutic Target Database are resources of curated chemistry-to-protein relationships widely used in the chemogenomic arena. In this work we have extended an earlier analysis (PMID 22821596) by comparing chemistry and protein target content between 2010 and 2013. For the former, details are presented for overlaps and differences, statistics of stereochemistry as well as stereo representation and MW profiles between the four databases. For 2013 our results indicate quality improvements, major expansion, increased achiral structures and changes in MW distributions. An orthogonal comparison of chemical content with different sources inside PubChem highlights further interpretable differences. Expansion of protein content by UniProt IDs is also recorded for 2013 and Gene Ontology comparisons for human-only sets indicate differences. These emphasise the expanding... - Egon Willighagen
Egon Willighagen
Quality Issues with Public Domain Chemogenomics Data - http://www.citeulike.org/user...
Molecular Informatics, Vol. 32, No. 11-12. (1 December 2013), pp. 898-905, doi:10.1002/minf.201300051 The key concept in chemogenomics is the similarity principle that states that similar ligands should bind similar targets. Chemogenomic analysis requires large amounts of data and both powerful computational algorithms and computers. Data used for chemogenomics analysis can either be compiled from open sources, or they can be produced in-house as is often done in the pharmaceutical industry. The chemogenomic modeller often has to resort to mixing activity values from different laboratories and even assay types to facilitate chemogenomic analysis. The amount of chemogenomics data available in the public domain has dramatically increased in recent years, allowing fully traceable analysis on a continuously increasing scale. However, some warning flags about the data quality have been raised and because the primary data determine the accuracy of chemogenomic analysis, the quality of the... - Egon Willighagen
Egon Willighagen
A Mitochondrial Expatriate: Nuclear Pyruvate Dehydrogenase - http://www.citeulike.org/user...
Cell, Vol. 158, No. 1. (July 2014), pp. 9-10, doi:10.1016/j.cell.2014.06.018 Vincent de Boer, Sander Houten - Egon Willighagen
Egon Willighagen
Adipsin Is an Adipokine that Improves β Cell Function in Diabetes - http://www.citeulike.org/user...
Cell, Vol. 158, No. 1. (July 2014), pp. 41-53, doi:10.1016/j.cell.2014.06.005 James Lo, Sanda Ljubicic, Barbara Leibiger, Matthias Kern, Ingo Leibiger, Tilo Moede, Molly Kelly, Diti Chatterjee Bhowmick, Incoronata Murano, Paul Cohen, Alexander Banks, Melin Khandekar, Arne Dietrich, Jeffrey Flier, Saverio Cinti, Matthias Blüher, Nika Danial, Per-Olof Berggren, Bruce Spiegelman - Egon Willighagen
Egon Willighagen
Mass Spectrometric Detection of Nanoparticle Host–Guest Interactions in Cells - http://www.citeulike.org/user...
Anal. Chem., Vol. 86, No. 13. (29 May 2014), pp. 6710-6714, doi:10.1021/ac501682y Synthetic host?guest chemistry is a versatile tool for biomedical applications. Characterization and detection of host?guest complexes in biological systems, however, is challenging due to the complexity of the biological milieu. Here, we describe and apply a mass spectrometric method to monitor the association and dissociation of nanoparticle (NP)-based host?guest interactions that integrates NP-assisted laser desorption/ionization (LDI) and matrix assisted laser desoption/ionization (MALDI) mass spectrometry. This LDI/MALDI approach reveals how NP surface functionality affects host?guest interactions in cells, information difficult to achieve using other techniques. Bo Yan, Gulen Yesilbag Tonga, Singyuk Hou, Patrick Fedick, Yi-Cheun Yeh, Felix Alfonso, Tsukasa Mizuhara, Richard Vachet, Vincent Rotello - Egon Willighagen
Egon Willighagen
Drosophila FoxP Mutants Are Deficient in Operant Self-Learning - http://www.citeulike.org/user...
PLoS ONE, Vol. 9, No. 6. (25 June 2014), e100648, doi:10.1371/journal.pone.0100648 Intact function of the Forkhead Box P2 (FOXP2) gene is necessary for normal development of speech and language. This important role has recently been extended, first to other forms of vocal learning in animals and then also to other forms of motor learning. The homology in structure and in function among the FoxP gene members raises the possibility that the ancestral FoxP gene may have evolved as a crucial component of the neural circuitry mediating motor learning. Here we report that genetic manipulations of the single Drosophila orthologue, dFoxP, disrupt operant self-learning, a form of motor learning sharing several conceptually analogous features with language acquisition. Structural alterations of the dFoxP locus uncovered the role of dFoxP in operant self-learning and habit formation, as well as the dispensability of dFoxP for operant world-learning, in which no motor learning occurs. These... - Egon Willighagen
Egon Willighagen
Ultrafast X-ray Auger probing of photoexcited molecular dynamics - http://www.citeulike.org/user...
Nature Communications, Vol. 5 (23 June 2014), doi:10.1038/ncomms5235 BK McFarland, JP Farrell, S Miyabe, F Tarantelli, A Aguilar, N Berrah, C Bostedt, JD Bozek, PH Bucksbaum, JC Castagna, RN Coffee, JP Cryan, L Fang, R Feifel, KJ Gaffney, JM Glownia, TJ Martinez, M Mucke, B Murphy, A Natan, T Osipov, VS Petrović, S Schorb, Th Schultz, LS Spector, M Swiggers, I Tenney, S Wang, JL White, W White, M Gühr - Egon Willighagen
Egon Willighagen
Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures - http://www.citeulike.org/user...
PeerJ, Vol. 1 (19 December 2013), e229, doi:10.7717/peerj.229 Amir Foroushani, Fiona Brinkman, David Lynn - Egon Willighagen
Egon Willighagen
Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases - http://www.citeulike.org/user...
BMC Medical Genomics, Vol. 2, No. 1. (2009), 2, doi:10.1186/1755-8794-2-2 BACKGROUND:The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular 'reactive oxygen species' (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation.REVIEW:We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many... - Egon Willighagen
Egon Willighagen
The rm2 metrics and regression through origin approach: Reliable and useful validation tools for predictive QSAR models (Commentary on ‘Is regression through origin useful in external validation of QSAR models?’) - http://www.citeulike.org/user...
European Journal of Pharmaceutical Sciences, Vol. 62 (October 2014), pp. 111-114, doi:10.1016/j.ejps.2014.05.019 Kunal Roy, Supratik Kar - Egon Willighagen
Egon Willighagen
Egonw: CAS numbers can have up to ten digits in the first part, according to the current FAQ. '''CAS Registry Numbers''',<ref>[http://www.cas.org/experti... CAS registry description], by the Chemical Abstracts Service</ref> also referred to as '''CASRNs''' and '''CAS Numbers''', are unique numerical [[identifier]]s assigned by the [[Chemical Abstracts Service]] to every chemical substance described in the open scientific literature (currently including those described from at least 1957 through the present), including [[Organic compounds|organic]] and [[inorganic compounds|inorganic]] compounds, [[mineral]]s, [[isotope]]s, [[alloys]] and nonstructurable materials (UVCBs, of unknown, variable composition, or biological origin).<ref name=crc>{{cite web | last = [[American Chemical Society]] | first = | authorlink = | coauthors = | title = CAS Registry and CASRNs | work = | publisher = | date = | url =... - Egon Willighagen
Egon Willighagen
Reshared post from Ravi Raja Merugu: - https://plus.google.com/1041867...
Original Post from Ravi Raja Merugu: Hello Dears,  Is there a way I can integrate molecular properties calculation module of CDK, into  a web application !! Im sure CDK is written in JAVA, but im more interested in knowing if these JAVA classes can be accessed through Javascript ? (like the way Jmol is handled by JS for web apps ) ..  Thanks in advance. - Egon Willighagen
Egon Willighagen
Stoichiometry of site-specific lysine acetylation in an entire proteome. - http://www.citeulike.org/user...
The Journal of biological chemistry (10 June 2014) Acetylation of lysine ε-amino groups influences many cellular processes and has been mapped to thousands of sites across many organisms. Stoichiometric information of acetylation is essential to accurately interpret biological significance. Here we developed and employed a novel method for directly quantifying stoichiometry of site-specific acetylation in the entire proteome of E. coli. By coupling isotopic labeling and a novel pairing algorithm, our approach performs an in silico enrichment of acetyl-peptides, circumventing the need for immunoenrichment. We investigated the function of the sole NAD+-dependent protein deacetylase, CobB, on both site-specific and global acetylation. We quantified 2206 peptides from 899 proteins and observed a wide distribution of acetyl-stoichiometry, ranging from less than 1% up to 98%. Bioinformatic analysis revealed that metabolic enzymes, which either utilize or generate acetyl-CoA, and proteins... - Egon Willighagen
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