MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'cheminformatics'. Sat, 03 Sep 2011 02:49:40 +0100 http://www.medworm.com/index.php?rid=4828965&cid=t_120465_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Flatest-science-news-with-a-spectral-twist.html Romantic notes – Cassis base 345B, undecavertol, 1,3-oxathiane oxane, isospirene… Perfume can be so romantic! But the chemical components underpinning the often-enticing and seductive smells of fragrances are, one might say equal parts art and science. One of the most intriguing elements of several fragrances, including popular perfumes like Le monde est beau by Daniela Andrier and DKNY Be Delicious by Maurice Roucel is the fruity top note – blackcurrant. Socioeconomic pollutants – How much socioeconomic factors affect exposure to persistent organic pollutants, especially during vulnerable periods of life such as pregnancy and childhood, is not yet well understood. A new study has investigated the relationship between maternal social class, based on occupation type,... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4828965 Mon, 16 May 2011 07:40:50 +0100 4828965 http://www.medworm.com/index.php?rid=4709237&cid=t_120465_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Frecent-science-news-roundup.html Optical catapulting for explosive fingerprint detection – Optical catapulting-laser-induced breakdown spectroscopy has been used to successfully detect residues of common explosives in human fingerprints, according to researchers from Egypt and Spain. Unsettling enzymes – Millisecond oscillations can massively impact how an enzyme functions, a new NMR spectroscopic study in the US reveals. The study suggests that finding ways to control such movements, without altering the overall structure of an enzyme might be useful in disabling an enzyme in disease. Proof of principle was demonstrated with an enzyme from Escherichia coli. Melanoma lead – Cheminformatics has helped researchers home in on a single compound that could lead to a new approach to treating malignant melanoma... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4709237 Thu, 14 Apr 2011 09:00:34 +0100 4709237 http://www.medworm.com/index.php?rid=4159275&cid=t_120465_107_f&fid=36672&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2FSciencebaseScienceBlog%2F%7E3%2FjTS2f09T_Fw%2Fcanned-heavy-metal-and-more.html My latest science news updates on SpectroscopyNOW – a sneak preview just for you ahead of their going live on 15th November, covering heavy metals in sardines, enzyme inhibitors for pain relief and sleep problems, the possibility of oral insulin without a Trojan horse carrier, and a spectroscopic test for male infertility that could explain the issue problem. Canned heavy metal – Samples of tinned sardines, originating from six countries have been analyzed for total arsenic, cadmium, lead and mercury content using spectroscopy. The analysis provides a useful baseline for a foodstuff – small pelagic fish – that could become increasingly important in a possible sustainable future and shows that arsenic rather than mercury could be the main concern in eating such smal... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=4159275 Fri, 12 Nov 2010 15:00:27 +0100 4159275 http://www.medworm.com/index.php?rid=3767110&cid=t_120465_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fspectral-science-news-3.html These are my links for July 15th from 12:27 to 12:32: Herpes invasion – There are eight herpes viruses that cause human diseases. Depending on how they affect us, they result in oral and genital herpes, the latter of which is present in almost a third of the US population. Currently, there is no cure for herpes viruses. Upon infection, the viruses remain in the body for life and can stay inactive for long periods of time. Herpes is also a leading cause of viral blindness and viral encephalitis. An X-ray study has now revealed the unusual structure of a key protein complex that allows a herpes virus to invade cells. Sweet sense of GOD – A glucose sensor based on a room-temperature ionic liquid rather than conventional solvents has much better acid-resistance than other sensors ... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=3767110 Mon, 19 Jul 2010 12:00:04 +0100 3767110 http://www.medworm.com/index.php?rid=2602024&cid=t_120465_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2Fstinging-heavy-metal-resistance.html Head-banging science news with a spectroscopic bent from my latest posts on the SpectroscopyNOW ezines, live June 15. A medical tale in the sting – The venom of the eusocial bee contains three novel antimicrobial compounds known as lasioglossins, which have been structurally characterised by NMR spectroscopy. The compounds offer a new avenue for developing new antibiotics that might defeat drug-resistant bacteria. Marine surfactant soaks up heavy metal – Atomic absorption spectroscopy (AAS) and other techniques have been used to demonstrate the effectiveness of a natural surfactant molecule in removing heavy metals from solutions for potential bioremediation applications. Topical resistance – Crystallography by UK scientists may have uncovered the mechanism by which quino... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=2602024 Wed, 15 Jul 2009 12:00:44 +0100 2602024 http://www.medworm.com/index.php?rid=1255232&cid=t_120465_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F02%2Fyet-another-life-science-informatics-ya.html There are yet another two new social Life Science Informatics (LSI) networking portals. In contrast to the already available LSI networking services are those technologically very mature and offer varieties of contribution and sharing possibilities for users.Wikia: Life Science InformaticsPlaxo: Life Science InformaticsBoth networking groups are looking for a stunning LSI logo, so please feel free making any suggestions. (Source: Mining Drug Space) Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1255232 Mon, 25 Feb 2008 18:49:00 +0100 1255232 http://www.medworm.com/index.php?rid=1238249&cid=t_120465_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F02%2Fsocial-search-in-drug-design-and-what.html Social search engines, another kind of social software, are trying to include user knowledge for improving search results in the future. One example is Wikia with an announcement of Jimmy WalesSearch is part of the fundamental infrastructure of the Internet. And we are making it open source. In contrast to the problem described by randfish might this improve search quality and reduce search engine tweaking requirements by users. Sometimes users have e.g. to multiply search terms or to find other tweaks, for getting the search results you want. Early initiatives like the the open directory project DMOZ (@Wikipedia) are using already user organized classification schemes for web links. SWiK organizes open source project information in a Wiki-like manner.I am still a little bit puzzled to und... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1238249 Sun, 17 Feb 2008 19:07:00 +0100 1238249 http://www.medworm.com/index.php?rid=1221368&cid=t_120465_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2008%2F02%2Fpipeline-pilot-student-edition.html As posted by Richard Compton on CCL.net provides SciTegic (part of Accelrys) a student version of Pipeline Pilot (PLP), which is free for academics ! I seriously like the thinking of those SciTegic guys, they are sharp, critical, and very trendy. This is a good starting point for having a hell of a discussion about science. Smart move, which is following the integration principle !This shows another fantastic example of a smart licensing strategy, which will probably always be critically discussed in the drug design area? Just recently there was a discussion on CCL and I commented on it. Anyway, this particular case will support science and allows scientists integrating their tools on a global level. Furthermore it allows sharing tools with industrial partner without forcing them creating ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1221368 Sun, 10 Feb 2008 23:26:00 +0100 1221368 http://www.medworm.com/index.php?rid=1147431&cid=t_120465_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F10%2Ffinding-job-in-cheminformatics-and.html From: jobs at ccl.net (do not send your application there!!!)To: jobs at ccl.netDate: Mon Sep 3 07:45:15 2007Subject: 07.09.03 Senior/Principal Scientist Molecular Modeling, Tibotec, Belgium Tibotec (http://www.tibotec.com) is a pharmaceutical research and development company with headquarters in Belgium and operating subsidiaries in the United States and Ireland. The company is a subsidiary of Johnson & Johnson. Tibotec is dedicated to the discovery and development of novel drugs for HIV/AIDS and other infectious diseases with the ultimate aim of enhancing and extending peoples lives.We currently are looking for a Senior or Principal Scientist Molecular Modeling and Cheminformatics, based at our headquarters in Mechelen, Belgium.In this function you will apply computational chemistry ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147431 Thu, 11 Oct 2007 19:29:00 +0100 1147431 http://www.medworm.com/index.php?rid=1147435&cid=t_120465_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fopen-source-tournament-rdkit-enters.html Egon is right! It is great that more and more open source tools are entering the drug design arena. On the other hand, we really need some benchmarking and feature comparisons for allowing to learn which tools should be used for which tasks.Noel dashed off an email to Greg Landrum, the main developer (who it turns out is also the developer of YAeHMOP (Yet Another extended Huckel Molecular Orbital Package) ), and he asked him what the story was. Two days ago, he returned from holidays and pointed Noel to the correct website and the documentation, and Noel couldn't believe what he was seeing...Some features that are cool:(1) Molecules based on the Boost Graph Library(2) All the Python stuff works for me on Windows!(3) 2D depiction!!!(4) 2D depiction that mimics 3D conformations!!!(5) 2D --> ... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147435 Fri, 14 Sep 2007 18:40:00 +0100 1147435 http://www.medworm.com/index.php?rid=1147437&cid=t_120465_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fsocial-chemistry-and-wikipedia.html As posted already are there still several problems with structure/substructure searches, and even the plain indexing of chemical structures within Wikipedia. Here are more details about it.==One==1.1. There are technical problems, because a SMILES code might contain characters reserved for the Wikipedia syntax.1.2. Some people dislike SMILES strings for large molecules1.3. It seems not to be easy to convince people about the relevance of unified chemical identifiers within Wikipedia, and subtructure and structure search link-outs. Especially the Wikipedia administration seems to be very skeptical and non-responsive.Substructure search in eMolecules and PubChem added I have added a SMILES based substructure search for eMolecules and PubChem. Please have a look at Cetirizine containing alrea... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147437 Wed, 12 Sep 2007 21:05:00 +0100 1147437 http://www.medworm.com/index.php?rid=1147438&cid=t_120465_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F09%2Fwikipedia-dbpedia-and-remaining.html At the beginning there was ... chaosI think many people know that I am a big fan of structured data mining. As highlighted by Noel and Peter are Wikis one way for collecting this kind of information on a global level. Wikis are also nice, because even the data structures (just part of the Wiki) might evolve.This idea is not new, but chemical data is still not there, yet! Yesterday, I was raising (again) the question what would be the best way to extend Wikipedia with structure searches? I was one of those establishing a first attempt enabling PubChem and eMolecules searches. I think you will agree that this is not general enough, because there are more databases out there. Especially, ChemSpider (@Wikipedia) is riding the web 2.0 wave very well, and it would be nice to see that even more s... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147438 Tue, 11 Sep 2007 18:26:00 +0100 1147438 http://www.medworm.com/index.php?rid=629285&cid=t_120465_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F118596625%2F From Joerg Kurt Wegner comes the news of JCTC tightening up their editorial policies. I am not on VPN right now, so I can’t access the editorial policy, but the assumption from the rest of the article is that the it is insufficient to report that a set of chemical data were analyzed, but some information about the methods used to analyze the data has to be included. While in itself, this does not guarantee open science, the bet here is that as journals up the ante on computational methods, commercial software will need to become more transparent about underlying methods, perhaps by publishing algorithms or by making source available (the latter is likely to be much more popular). And Joerg is correct when he says that software that allows for easy prototyping and scripting (a reason ... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=629285 Tue, 22 May 2007 17:55:34 +0100 629285