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Egon Willighagen › Comments

Egon Willighagen
NMR Crystallography of Enzyme Active Sites: Probing Chemically Detailed, Three-Dimensional Structure in Tryptophan Synthase - http://www.citeulike.org/user...
Acc. Chem. Res., Vol. 46, No. 9. (28 March 2013), pp. 2008-2017, doi:10.1021/ar3003333 NMR crystallography?the synergistic combination of X-raydiffraction, solid-state NMR spectroscopy, and computational chemistry?offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate.Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5?2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts... - Egon Willighagen
Egon Willighagen
Chemistry Development Kit - http://en.wikipedia.org/w...
Egonw: Added the quite a lot cited PaDEL. {{Infobox software | name = Chemistry Development Kit | logo = [[Image:Cdklogo.svg|200px]] | screenshot = | caption = | developer = The CDK Project | released = {{Start date and age|df=yes|2001|05|11}}<ref>https://sourceforge.net/project...</ref> | frequently updated = yes<!-- Release version update? Don't edit this page, just click on the version number! --> | programming language = [[Java (programming language)]] | operating system = [[Cross-platform]] | platform = | language = | genre = [[Chemoinformatics]]/[[Molecular modelling]]/[[Bioinformatics]] | license = [[GNU Lesser General Public License]] | website = http://cdk.sourceforge.net/ }} The '''Chemistry Development Kit''' is an [[open-source]] Java library for [[Chemoinformatics]] and [[Bioinformatics]].<ref>{{cite journal |author=Steinbeck, C.; Han, Y.Q.; Kuhn, S.; Horlacher, O.; Luttmann, E.; Willighagen, E.L. |title=The Chemistry Development Kit (CDK): An... - Egon Willighagen
Egon Willighagen
An overview of FDA-approved new molecular entities: 1827-2013. - http://www.citeulike.org/user...
Drug discovery today, Vol. 19, No. 8. (August 2014), pp. 1033-1039 The pharmaceutical industry is undergoing fundamental change and its future is unclear. We performed a meta-analysis by cataloging FDA-approved legacy drugs and new molecular entities (NMEs). Objective information regarding scientific, medical and commercial activities was captured and provides insight into processes governing drug development. In this report, we review the rates of NME introduction through to the end of 2013. Recent trends show the emergence of a handful of companies that controls two-thirds of NMEs. We also report growth in the number of NMEs controlled by marketing organizations that have little or no internal drug discovery or development activities. This trend has increased dramatically since 2000 and could raise important questions about the future landscape and viability of drug discovery and development. Copyright © 2014 Elsevier Ltd. All rights reserved. Michael Kinch, Austin Haynesworth,... - Egon Willighagen
Egon Willighagen
Molecular Biology Turns Into Chemistry http://pipeline.corante.com/archive... About this Author. DBL%20Hendrix%20small.png College chemistry, 1983. Derek Lowe The 2002 Model Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . . Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in ... - Egon Willighagen
Egon Willighagen
Introducing miniCRAN: an R package to create a private CRAN repository http://feedly.com/e/m26dc4CS - https://plus.google.com/1041867...
Introducing miniCRAN: an R package to create a private CRAN repository http://feedly.com/e/m26dc4CS by Andrie deVries One of the reasons that R is so popular is the CRAN archive of useful packages. However, with more than 5,900 packages on CRAN, many organisations need to maintain a private mirror of CRAN with only a subset of packages that are relevant to them. The package miniCRAN makes this possible by determining the dependency tree for a given set of packages, then downloading all of the package dependencies. (My previous post showed how t... - Egon Willighagen
Egon Willighagen
Open Source Malaria has completed an experiment in crowdsourcing for open drug discovery. Identifying and developing medicines is a labour-intensive process, particularly in the discovery and optim... - Egon Willighagen
Egon Willighagen
ResearchGate keeps disappointing me. In principle it could be a great platform, but the manage to get... - https://plus.google.com/1041867...
ResearchGate keeps disappointing me. In principle it could be a great platform, but the manage to get too many things just wrong. Like the above feature. Cool they consider crowdsourcing citation data! But (besides that I wonder where one could download that citation data): * I cannot reject and only confirm. WTF??? * I cannot inform Varun Dewaker accidentally made a link to the wrong paper (Bioclipse-R doesn’t cite that paper) So, the only thing I can do here is ignore, which is not really helpful, not for the quality of their database, not for Dr Dewaker. ResearchGate keeps disappointing me. In principle it could be a great platform, but the manage to get too many things just wrong. Like the above feature. Cool they consider crowdsourcing citation... - Egon Willighagen
Egon Willighagen
Collaborative browser-based tools aim to change the way researchers write and publish their papers. - Egon Willighagen
Egon Willighagen
Example NanoWiki data that is going into the eNanoMapper prototype database. - Egon Willighagen
Egon Willighagen
Jenkins-CI: automating lab processes Our group organizes public Science Cafes where people from Maastricht... - https://plus.google.com/1041867...
Jenkins-CI: automating lab processes Our group organizes public Science Cafes where people from Maastricht University can see the research it is involved in. Yesterday it was my turn again, and I gave a presentation showing the BiGCaT and eNanoMapper Jenkins-CI installations (set up by Nuno) w... Our group organizes public Science Cafes where people from Maastricht University can see the research it is involved in. Yesterday it was my turn again, and I gave a presentation showing the BiGCaT and eNanoMapper Jenkins-CI ... - Egon Willighagen
Egon Willighagen
Reshared post from Ioannis Moutsatsos: - https://plus.google.com/1041867...
Original Post from Ioannis Moutsatsos: Recording of my recent presentation from the 2014 Jenkins User Conference in Boston. I presented on how I've used the Jenkins-CI as a scientific image and data processing platform. It should be of interest to anyone interested in life-science data management and analytics. JUC- Boston: Jenkins CI, as a Scientific Data and Image Processing Platform - Egon Willighagen
Benjamin Good
Conference proceedings are citable, stop double-dipping - http://i9606.blogspot.com/2014...
I agree. Sadly, many life science faculties don't count proceedings, even if heavily peer reviewed. That is, they *expect* you to do the double-dipping and just don't count the first dip. - Egon Willighagen
Egon Willighagen
Transcriptome analysis of peripheral blood mononuclear cells in human subjects following a 36 h fast provides evidence of effects on genes regulating inflammation, apoptosis and energy metabolism - http://www.citeulike.org/user...
In Genes &#38; Nutrition, Vol. 9, No. 6. (2014), pp. 1-11, doi:10.1007/s12263-014-0432-4 There is growing interest in the potential health benefits of diets that involve regular periods of fasting. While animal studies have provided compelling evidence that feeding patterns such as alternate-day fasting can increase longevity and reduce incidence of many chronic diseases, the evidence from human studies is much more limited and equivocal. Additionally, although several candidate processes have been proposed to contribute to the health benefits observed in animals, the precise molecular mechanisms responsible remain to be elucidated. The study described here examined the effects of an extended fast on gene transcript profiles in peripheral blood mononuclear cells from ten apparently healthy subjects, comparing transcript profiles after an overnight fast, sampled on four occasions at weekly intervals, with those observed on a single occasion after a further 24 h of fasting. Analysis of... - Egon Willighagen
Egon Willighagen
On the eve of the closing of the European Consultation on Science 2.0, LIBER has issued a statement both welcoming the Consultation as a step towards strengthening the competitiveness of European research, and calling on the European Commission to take measures towards enabling Open Science. In commenting on the position statement, LIBER President, Ms. Kristiina… - Egon Willighagen
Egon Willighagen
This blog has been a bit silently lately. Fairly, I have been running Linux at Maastricht University for 2.5 years now, without much problems. Perhaps the least pleasing thing is the lack of UM-styled templates and the horren... - Egon Willighagen
Egon Willighagen
The nature and composition of the Linux kernel developer community: a dynamic analysis - http://www.citeulike.org/user...
SIEPR-Project NOSTRA Working Paper (21st February) (2003) Rishab Ghosh, Paul David - Egon Willighagen
Egon Willighagen
The open source code movement: the Linux operating system - http://www.citeulike.org/user...
Multi-Organizational Partnerships and Cooperative Strategy (2000), pp. 283-287 Marc van Wegberg, Peter Berends - Egon Willighagen
Egon Willighagen
Reshared post from Mark Fortner: - https://plus.google.com/1041867...
Original Post from Mark Fortner: DukeScript brings Java to HTML5, JavaScript http://www.javaworld.com/article... Framework lets developers leverage Java while building HTML5 and JavaScript applications - Egon Willighagen
Egon Willighagen
Biological network extraction from scientific literature: state of the art and challenges - http://www.citeulike.org/user...
Briefings in Bioinformatics, Vol. 15, No. 5. (01 September 2014), pp. 856-877, doi:10.1093/bib/bbt006 Networks of molecular interactions explain complex biological processes, and all known information on molecular events is contained in a number of public repositories including the scientific literature. Metabolic and signalling pathways are often viewed separately, even though both types are composed of interactions involving proteins and other chemical entities. Chen Li, Maria Liakata, Dietrich Rebholz-Schuhmann - Egon Willighagen
Egon Willighagen
Surface Functionalization of Semiconductor and Oxide Nanocrystals with Small Inorganic Oxoanions (PO43–, MoO42–) and Polyoxometalate Ligands - http://www.citeulike.org/user...
ACS Nano, Vol. 8, No. 9. (24 August 2014), pp. 9388-9402, doi:10.1021/nn503458y In this work, we study the functionalization of the nanocrystal (NC) surface with inorganic oxo ligands, which bring a new set of functionalities to all-inorganic colloidal nanomaterials. We show that simple inorganic oxoanions, such as PO43? and MoO42?, exhibit strong binding affinity to the surface of various II?VI and III?V semiconductor and metal oxide NCs. ?-Potential titration offered a useful tool to differentiate the binding affinities of inorganic ligands toward different NCs. Direct comparison of the binding affinity of oxo and chalcogenidometallate ligands revealed that the former ligands form a stronger bond with oxide NCs (e.g., Fe2O3, ZnO, and TiO2), while the latter prefer binding to metal chalcogenide NCs (e.g., CdSe). The binding between NCs and oxo ligands strengthens when moving from small oxoanions to polyoxometallates (POMs). We also show that small oxo ligands and POMs make it... - Egon Willighagen
Egon Willighagen
Now, if only the manage to make a 3D lenses system that can be put around the full hand.... (PS. I think... - https://plus.google.com/1041867...
Now, if only the manage to make a 3D lenses system that can be put around the full hand.... (PS. I think there is a direct line of sight in the middle, so this is a bit of cheating too). Still, cool! Doctoral student Joseph Choi is pictured with a a multidirectional `perfect paraxial' cloak using 4 lenses. Inspired perhaps by Harry Potter's invisibility cloak, scientists have recently developed several ways—some simple and some involving new technologies—to hide objects from view. - Egon Willighagen
Egon Willighagen
CODATA/VAMAS Joint Working Group on the Description of Nanomaterials - CODATA - Egon Willighagen
Egon Willighagen
What do astronauts, a towel and a paranoid android have in common? The answer is 42. The International Space Station's Expedition 42 crew has featured the link between their numerical designation and "The Hitchhiker's Guide to the Galaxy" on a poster and - Egon Willighagen
Egon Willighagen
Attending the opening of the #MaCSBio... The primary aim of MaCSBio is to facilitate the integration of relevant biological data coming from different empirical domains using mathematical multi-scale modelling approaches. This will take shape in two research lines, which will be established within the centre. - Egon Willighagen
Egon Willighagen
Slides at the Open PHACTS community workshop (June 26) First MSP graduates . It seems had not posted... - https://plus.google.com/1041867...
Slides at the Open PHACTS community workshop (June 26) First MSP graduates . It seems had not posted my slides yet of the presentation at the 6th Open PHACTS community workshop . At this meeting I gave an overview of the Programming in the Life Sciences course we give to 2nd and 3rd students of the Maastricht S... First MSP graduates. It seems had not posted my slides yet of the presentation at the 6th Open PHACTS community workshop. At this meeting I gave an overview of the Programming in the Life Sciences course we give to 2nd and 3r... - Egon Willighagen
Egon Willighagen
CC-BY 2.0 by Dmitry Valberg. Where the OpenTox Europe 2013 presentation focused on the technical layers of Open PHACTS, this presentation addressed a key knowledge management solution to scientific questions and the Open PHAC... - Egon Willighagen
Egon Willighagen
Reshared post from Authorea *: - https://plus.google.com/1041867...
Strong competition! Shared LaTeX authoring is flying! Original Post from Authorea *: We believe that the article of the future is more than just text and images Authorea, a startup that's aiming to shake up the staid scientific publication process -- of learned journals and lengthy peer reviews -- with a digital.. - Egon Willighagen
Egon Willighagen
Physiological role for nitrate-reducing oral bacteria in blood pressure control - http://www.citeulike.org/user...
Free Radical Biology and Medicine, Vol. 55 (February 2013), pp. 93-100, doi:10.1016/j.freeradbiomed.2012.11.013 Vikas Kapil, Syed Haydar, Vanessa Pearl, Jon Lundberg, Eddie Weitzberg, Amrita Ahluwalia - Egon Willighagen
Pierre Lindenbaum
hello frienfeed, twitter is down.
Twitter seems to work for me right now... (2 hours after your FF post) - Egon Willighagen
Egon Willighagen
Dear Jon, it is important that you bring up peer review in this context. One aspect of papers in higher... - https://plus.google.com/1041867...
Dear Jon, it is important that you bring up peer review in this context. One aspect of papers in higher impact journal is the tendency (anecdotal too) that the higher the impact the less detail given, but more importantly, the amount of results presented. It would not surprise me, however, if the amount of time spent on reviews does not linearly scale with the amount of results presented. Seriously, who can expect reviewers to accurately peer review a full genome. I expect reviewers to assume a lot methods to be applied properly. But the amount of results is not the only issue; I think the multidisciplinary scope of the results also make it unfeasible that two, three, or even four reviewers can accurately review all the results presented in the paper. I short, I hereby postulate that the underlying mechanism is that higher impact attracts more results and moreover results of higher complexity, resulting on putting increased requirements on the skills and time resources of the... - Egon Willighagen
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