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Egon Willighagen › Comments

Egon Willighagen
Energy-filtered cold electron transport at room temperature - http://www.citeulike.org/user...
Nature Communications, Vol. 5 (10 September 2014), 4745, doi:10.1038/ncomms5745 Pradeep Bhadrachalam, Ramkumar Subramanian, Vishva Ray, Liang-Chieh Ma, Weichao Wang, Jiyoung Kim, Kyeongjae Cho, Seong Koh - Egon Willighagen
Egon Willighagen
Writing template code to calculate a set of molecular properties with the CDK. - Egon Willighagen
Egon Willighagen
Atomic Physicochemical Parameters for Three-Dimensional Structure-Directed Quantitative Structure-Activity Relationships I. Partition Coefficients as a Measure of Hydrophobicity - http://www.citeulike.org/user...
Journal of Computational Chemistry, Vol. 7, No. 4. (August 1986), pp. 565-577, doi:10.1002/jcc.540070419 Earlier we showed (A. K. Ghose and G. M. Crippen, J. Med. Chem., 28, 333, 1985) the necessity of atomic physicochemical parameters in three-dimensional receptor mapping. Here we derive more refined and widely applicable hydrophobicity parameters. Carbon, hydrogen, oxygen, nitrogen, sulfur, and halogens are classified into 110 atom types. Among these, the hydrophobic contributions of 90 atom types have been evaluated from the log P(water-octanol) values of 494 molecules, using the additive model and leastsquares technique. It gave a standard deviation of 0.347, a correlation coefficient of 0.962, and an explained variance of 0.908. These atomic values were used to predict the log P values of 69 compounds. The predicted values showed a standard deviation of 0.404 and a correlation coefficient of 0.896. This work has been compared with more conventional approaches. Arup Ghose, Gordon... - Egon Willighagen
Egon Willighagen
Chemical applications of graph theory - http://www.citeulike.org/user...
(1976) Alexandru Balaban - Egon Willighagen
Egon Willighagen
+John May, this (old) blogpost shows some of the things needed by Bioclipse. - https://plus.google.com/1041867...
+John May, this (old) blogpost shows some of the things needed by Bioclipse. The Bioclipse Team is proud to announce the release of Bioclipse 2.2.0. The new version includes, apart from numerous bug fixes, the following highlights: * Cheminformatics, with a pure SWT-based chemical 2D editor (JChemPain... - Egon Willighagen
Egon Willighagen
"DIY: make your own homunculus" Pretty cool science-at-home experiment! (in Dutch) - https://plus.google.com/1041867...
"DIY: make your own homunculus" Pretty cool science-at-home experiment! (in Dutch) Je vingertoppen zijn veel gevoeliger dan je bovenarm. Waarom eigenlijk? Dit heeft te maken met de organisatie van je zenuwen en de zogenaamde sensorische cortex in je hersenen. In dat stukje van de... - Egon Willighagen
Egon Willighagen
Disappointing that G+ cannot handle SVG images... see them for real here: https://github.com/cdk/cdk... - https://plus.google.com/1041867...
Disappointing that G+ cannot handle SVG images... see them for real here: https://github.com/cdk... camo.githubusercontent.com/51a019d85ae365e07a44c10c6fcb94485cb97452/687474703a2f2f63646b2e6769746875622e696f2f63646b2f696d672f73746467656e2f43484542495f333231352e737667 - Egon Willighagen
Egon Willighagen
Factors affecting citation rates of research articles - http://www.citeulike.org/user...
Journal of the Association for Information Science and Technology (June 2014), pp. n/a-n/a, doi:10.1002/asi.23209 Natsuo Onodera, Fuyuki Yoshikane - Egon Willighagen
Egon Willighagen
Reshared post from Mark Fortner: - https://plus.google.com/1041867...
Wisdom from the old continent... Original Post from Mark Fortner: "The Surprising Reason Why Bike Lanes Could Be Good For Cars" http://feedly.com/e/Wz-HHK3f It's the typical saga unfolding in every city in America. Bike lanes go in, often replacing a lane of vehicular traffic. Drivers get mad, claiming that the presence of bike lanes is destroying their commute. But according to one study, bike lanes may actually be making life better for drivers. - Egon Willighagen
Egon Willighagen
Authors: Theo van Veen and Sieta Neuerburg According to the National library of the Netherlands, libraries are positioned at the very core of the Semantic Web. In the words of Hans Jansen, Head of ... - Egon Willighagen
Egon Willighagen
Open knowledge dissemination (with @IFTTT) An important part of science is communication. That is why... - https://plus.google.com/1041867...
Open knowledge dissemination (with @IFTTT) An important part of science is communication. That is why we publish. New insights are useless if they sit on some desk. Instead, reuse counts. This communication is not just about the facts, but also a means to establish research networks. Efficient resea... An important part of science is communication. That is why we publish. New insights are useless if they sit on some desk. Instead, reuse counts. This communication is not just about the facts, but also a means to establish re... - Egon Willighagen
Egon Willighagen
Door grondstoffen te winnen uit algen kunnen veel bedrijven duurzamer en op termijn wellicht goedkoper te werk gaan. Maar de techniek bevindt zich nog ... - Egon Willighagen
Egon Willighagen
Synthesis of complex intermediates for the study of a dehydratase from borrelidin biosynthesis - http://www.citeulike.org/user...
Beilstein Journal of Organic Chemistry, Vol. 10 (11 March 2014), pp. 634-640, doi:10.3762/bjoc.10.55 Frank Hahn, Nadine Kandziora, Steffen Friedrich, Peter Leadlay - Egon Willighagen
Egon Willighagen
Yesterday I shared a spreadsheet containing references to 497 papers on Ebola including the access and license type of each paper. These were crowdsourced by a group of us over a period of a week. - Egon Willighagen
Egon Willighagen
First steps in Open Notebook Science Scheme 2 from this Beilstein Journal of Organic Chemistry paper... - https://plus.google.com/1041867...
First steps in Open Notebook Science Scheme 2 from this Beilstein Journal of Organic Chemistry paper by Frank Hahn et al . I blogged a few weeks back I blogged about my first Open Notebook Science entry . The post suggest I will look at a few ONS service providers, but, honestly,  Open Noteboo... Scheme 2 from this Beilstein Journal of Organic Chemistry paper by Frank Hahn et al. I blogged a few weeks back I blogged about my first Open Notebook Science entry. The post suggest I will look at a few ONS service providers... - Egon Willighagen
Egon Willighagen
Reshared post from Ilya Grigorik: - https://plus.google.com/1041867...
I wish we had a diagram like this too for Java! Original Post from Ilya Grigorik: Know thy (Linux) perf tools: http://bit.ly/1t69Uwy - perhaps the most comprehensive overview I've ever come across.  linux_observability_tools.png - Egon Willighagen
Egon Willighagen
Mmm... this pathways needs some serious metabolite identifier hacking... - https://plus.google.com/1041867...
Mmm... this pathways needs some serious metabolite identifier hacking... Proteome-based systems biology analysis of the diabetic mouse aorta reveals major changes in Fatty Acid biosynthesis as potential hallmark in diabetes mellitus-associated vascular disease. Husi H, Van... - Egon Willighagen
Egon Willighagen
Reshared post from Egon Willighagen: - https://plus.google.com/1041867...
Original Post from Egon Willighagen: Post WikiPathways contributions to Twitter - Egon Willighagen
Egon Willighagen
Post WikiPathways contributions to Twitter - Egon Willighagen
Egon Willighagen
NWO wijst talent af met foute argumenten en ontmoedigt zo de wetenschappelijke avonturiers, meent hoogleraar Willem Trommel. De Nederlandse ... - Egon Willighagen
Egon Willighagen
BMC systems biology, Vol. 8, No. 1. (15 August 2014) BioModels Database is a reference repository of mathematical models used in biology. Models are stored as SBML files on a file system and metadata is provided in a relational database. Models can be retrieved through a web interface and programmatically via web services. In addition to those more traditional ways to access information, Linked Data using Semantic Web technologies (such as the Resource Description Framework, RDF), is becoming an increasingly popular means to describe and expose biological relevant data. We present the BioModels Linked Dataset, which exposes the models' content as a dereferencable interlinked dataset. BioModels Linked Dataset makes use of the wealth of annotations available within a large number of manually curated models to link and integrate data and models from other resources. The BioModels Linked Dataset provides users with a dataset interoperable with other semantic web resources. It supports... - Egon Willighagen
Egon Willighagen
Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS - http://www.citeulike.org/user...
Mass Spectrometry, Vol. 3, No. Special_Issue_2. (2014), pp. S0036-S0036, doi:10.5702/massspectrometry.s0036 Emma Schymanski, Michael Gerlich, Christoph Ruttkies, Steffen Neumann - Egon Willighagen
Egon Willighagen
Ten Simple Rules for Providing a Scientific Web Resource - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 7, No. 5. (26 May 2011), e1001126, doi:10.1371/journal.pcbi.1001126 Sebastian Schultheiss - Egon Willighagen
Egon Willighagen
Exploiting open data: a new era in pharmacoinformatics - http://www.citeulike.org/user...
Future Medicinal Chemistry, Vol. 6, No. 5. (April 2014), pp. 503-514, doi:10.4155/fmc.14.13 Daria Goldmann, Floriane Montanari, Lars Richter, Barbara Zdrazil, Gerhard Ecker - Egon Willighagen
Egon Willighagen
Quantum imaging with undetected photons - http://www.citeulike.org/user...
Nature, Vol. 512, No. 7515. (27 August 2014), pp. 409-412, doi:10.1038/nature13586 Gabriela Lemos, Victoria Borish, Garrett Cole, Sven Ramelow, Radek Lapkiewicz, Anton Zeilinger - Egon Willighagen
Egon Willighagen
Sliding Rocks on Racetrack Playa, Death Valley National Park: First Observation of Rocks in Motion - http://www.citeulike.org/user...
PLoS ONE, Vol. 9, No. 8. (27 August 2014), e105948, doi:10.1371/journal.pone.0105948 The engraved trails of rocks on the nearly flat, dry mud surface of Racetrack Playa, Death Valley National Park, have excited speculation about the movement mechanism since the 1940s. Rock movement has been variously attributed to high winds, liquid water, ice, or ice flotation, but has not been previously observed in action. We recorded the first direct scientific observation of rock movements using GPS-instrumented rocks and photography, in conjunction with a weather station and time-lapse cameras. The largest observed rock movement involved >60 rocks on December 20, 2013 and some instrumented rocks moved up to 224 m between December 2013 and January 2014 in multiple move events. In contrast with previous hypotheses of powerful winds or thick ice floating rocks off the playa surface, the process of rock movement that we have observed occurs when the thin, 3 to 6 mm, “windowpane” ice sheet covering... - Egon Willighagen
Egon Willighagen
A crystallographic perspective on sharing data and knowledge - http://www.citeulike.org/user...
In Journal of Computer-Aided Molecular Design (2014), pp. 1-8, doi:10.1007/s10822-014-9780-9 The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to... - Egon Willighagen
Egon Willighagen
The Major Cow Milk Allergen Bos d 5 Manipulates T-Helper Cells Depending on Its Load with Siderophore-Bound Iron - http://www.citeulike.org/user...
PLoS ONE, Vol. 9, No. 8. (12 August 2014), e104803, doi:10.1371/journal.pone.0104803 The mechanisms of allergic sensitization to milk are still elusive. The major allergen Bos d 5 belongs to the lipocalin-family and thus is able to transport numerous ligands. In this study we investigated its ability to bind to iron-siderophore complexes and tested the immune-modulatory properties of Bos d 5 in either forms. Structural and in silico docking analysis of Bos d 5 revealed that Bos d 5 is able to bind to iron via catechol-based flavonoids (quercetin, myricetin, luteolin) that act as siderophores as confirmed by spectral-analysis and iron staining. Calculated dissociation constants of docking analyses were below 1 µM by virtual addition of iron. When incubated with human peripheral blood mononuclear cells (PBMCs), only the apo-form of Bos d 5 led to an increase of CD4+positive cells and significantly elevated IL13 and IFNγ-levels. In contrast, holo-Bos d 5 decreased numbers of CD4... - Egon Willighagen
Egon Willighagen
Light Harvesting: Near-Infrared Harvesting Transparent Luminescent Solar Concentrators (Advanced Optical Materials 7/2014) - http://www.citeulike.org/user...
Advanced Optical Materials, Vol. 2, No. 7. (July 2014), pp. 599-599, doi:10.1002/adom.201470040 Yimu Zhao, Garrett Meek, Benjamin Levine, Richard Lunt - Egon Willighagen
Egon Willighagen
Electron microscopy of gold nanoparticles at atomic resolution - http://www.citeulike.org/user...
Science, Vol. 345, No. 6199. (22 August 2014), pp. 909-912, doi:10.1126/science.1251959 Adding only a few atoms or changing the capping ligand can dramatically change the structure of individual metal nanoparticles. Azubel et al. used aberration-corrected transmission electron microscopy to derive a three-dimensional reconstruction of water-soluble gold nanoparticles. Small-angle x-ray scattering and other techniques have also corroborated this model. They used this to determine the atomic structure, which compared favorably with density functional theory calculations, without assuming any a priori structural knowledge or the use of model fitting. Maia Azubel, Jaakko Koivisto, Sami Malola, David Bushnell, Greg Hura, Ai Koh, Hironori Tsunoyama, Tatsuya Tsukuda, Mika Pettersson, Hannu Häkkinen, Roger Kornberg - Egon Willighagen
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