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  • November 30, 2015
  • 07:01 AM

How Spicy Would You Like That Chemotherapy?

by Shane Caldwell in Helical Translations

A molecule from chili peppers can be modified to bind to a protein involved in cancer progression. How would a molecule similar to hot pepper spice be used to fight cancer?... Read more »

  • June 6, 2015
  • 06:31 AM

Humidity Powered Energy

by Viputheshwar Sitaraman in Draw Science

We can now power low energy devices using humidity! Scientists harnessed bacteria that shrink in response to changes in humidity to generate energy.... Read more »

Yuan, T., Ormonde, C., Kudlacek, S., Kunche, S., Smith, J., Brown, W., Pugliese, K., Olsen, T., Iftikhar, M., Raston, C.... (2015) Shear-Stress-Mediated Refolding of Proteins from Aggregates and Inclusion Bodies. ChemBioChem. DOI: 10.1002/cbic.201402427  

  • March 11, 2015
  • 04:57 PM

Why do we remember bad memories easier than good ones?

by Crystals and Catalysts in Crystals and Catalysts

How many times have you found yourself recollecting a bad memory?It doesn't even have to be a very bad memory,  it could be a sad moment, a moment which angered you or even an embarrassing moment. But it is definitely prominent in your mind.All of these things could have happened years ago and you don't want to remember them but they still come back and haunt you from time to time.But the question is why do we remember  these bad memories more than good ones? Time to think ou........ Read more »

Ritchie TD, Batteson TJ, Bohn A, Crawford MT, Ferguson GV, Schrauf RW, Vogl RJ, & Walker WR. (2015) A pancultural perspective on the fading affect bias in autobiographical memory. Memory (Hove, England), 23(2), 278-90. PMID: 24524255  

  • February 3, 2015
  • 11:54 AM

How to Unboil an Egg

by Viputheshwar Sitaraman in Draw Science

How to unboil an egg...and why it matters: Scientists have discovered how to refold proteins easily; this could change the face of protein synthesis!... Read more »

Yuan, T., Ormonde, C., Kudlacek, S., Kunche, S., Smith, J., Brown, W., Pugliese, K., Olsen, T., Iftikhar, M., Raston, C.... (2015) Shear-Stress-Mediated Refolding of Proteins from Aggregates and Inclusion Bodies. ChemBioChem. DOI: 10.1002/cbic.201402427  

  • July 2, 2014
  • 03:54 PM

Plant = Pill?

by Viputheshwar Sitaraman in Draw Science

E. Longfolia: an aphrodisiac, anti-inflammatory, and anti-malarial miracle plant. [Infographic]... Read more »

Tran TV, Malainer C, Schwaiger S, Atanasov AG, Heiss EH, Dirsch VM, & Stuppner H. (2014) NF-κB inhibitors from Eurycoma longifolia. Journal of natural products, 77(3), 483-8. PMID: 24467387  

  • February 21, 2014
  • 04:43 AM

Slow publishing innovation

by egonw in Chem-bla-ics

Elsevier is not the only publisher with a large innovation inertia. In fact, I think many large organizations do, particularly if there are too many interdependencies, causing too long lines. Greg Laundrum made me aware that one American Chemical Society journal is now going to encourage (not require) machine readable forms of chemical structures to be included in their flagship. The reasoning by Gilson et al. is balanced. It is also 15 years too late. This question was relevant at the end of th........ Read more »

Gilson MK, Georg G, & Wang S. (2014) Digital Chemistry in the Journal of Medicinal Chemistry. Journal of medicinal chemistry. PMID: 24521446  

  • February 19, 2014
  • 01:16 AM

Hyperpolarization without persistent radicals

by Mr. Sit and Spin in Sit and Spin

The paper for this week is"Hyperpolarization without persistent radical for in vivo real-time metabolic imaging"byEichhorn, Takado, Salameh, Capozzi, Cheng, Hyacinthe, Mishkovsky, Roussel and CommentPNAS 2013 110 18064 is a lot going on in this short and well-written paper.  I highly recommend that you read it yourself, because I don't quite know where to start.  I guess I have to start somewhe........ Read more »

Eichhorn TR, Takado Y, Salameh N, Capozzi A, Cheng T, Hyacinthe JN, Mishkovsky M, Roussel C, & Comment A. (2013) Hyperpolarization without persistent radicals for in vivo real-time metabolic imaging. Proceedings of the National Academy of Sciences of the United States of America, 110(45), 18064-9. PMID: 24145405  

  • January 22, 2013
  • 04:09 AM

ToxBank: the next generation toxicology

by egonw in Chem-bla-ics

Before I moved to my current position in Maastricht, I had the great pleasure to work with Prof. Roland Grafström (check his pathway bioinformatics done with his then PhD Rebecca) and Prof. Bengt Fadeel at the Karolinska Institutet. During this year I part-time worked on ToxBank and part-time on nano-QSAR, and worked on semantics, predictive toxicology, and Open Data. This blog post is about the ToxBank work.

I promised firework, and the first rockets are heading upw........ Read more »

Kohonen, P., Benfenati, E., Bower, D., Ceder, R., Crump, M., Cross, K., Grafström, R., Healy, L., Helma, C., Jeliazkova, N.... (2013) The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing. Molecular Informatics. DOI: 10.1002/minf.201200114  

  • September 22, 2012
  • 11:02 AM

OMG! An Open Molecule Generator!

by egonw in Chem-bla-ics

Earlier this week an important cheminformatics paper appeared in the Journal of Cheminformatics. It is about the Open Molecule Generator (see below for the paper). This was one important piece of functionality still missing from Open Source cheminformatics. This works uses the Chemistry Development Kit, and was written by Julio Peironcely.

The Analytical Biosciences' group of Prof. Hankemeier (and many others, including also Theo Reijmers) and funded by the Netherlands Metab........ Read more »

Julio E Peironcely, Miguel Rojas-Chertó, Davide Fichera, Theo Reijmers, Leon Coulier, Jean-Loup Faulon, & Thomas Hankemeier. (2012) OMG: open molecule generator. Journal of Cheminformatics, 21. DOI: 10.1186/1758-2946-4-21  

  • July 20, 2012
  • 04:16 PM

Researchers find new anti-malarial drug target

by admin in Beaker

An international team of scientists, including researchers at the University of California, San Diego and Sanford-Burnham Medical Research Institute, have identified the first reported inhibitors of a key enzyme involved in survival of the parasite responsible for malaria.... Read more »

Janina Preuss, Patrick Maloney, Satyamaheshwar Peddibhotla, Michael P. Hedrick, Paul Hershberger, Palak Gosalia, Monika Milewski, Yujie Linda Li, Eliot Sugarman, Becky Hood.... (2012) Discovery of a Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase inhibitor (R,Z)-N-((1-ethylpyrrolidin-2-yl)methyl)-2-(2-fluorobenzylidene)-3-oxo-3,4-dihydro-2H-benzo[b][1,4]thiazine-6-carboxamide (ML276) that reduces paras. Journal of Medicinal Chemistry. info:/10.1021/jm300833h

  • July 18, 2012
  • 05:57 PM

The Summer Olympics and the “War on Doping”

by Dirk Hanson in Addiction Inbox

Time for a change in strategy?

The Summer Olympics are fast approaching, and that can only mean one thing: drugs. After more than a decade, you might wonder, how goes the so-called “War on Doping?”

Not so good, but thanks for asking. The World Anti-Doping Agency, established in 1999 and backed by the UNESCO anti-doping convention, will be operating 24/7 during the games, protecting the “purity” of Sport, trying to ferret out everything from cannabis and cocaine to steroids and ........ Read more »

Kayser B, & Broers B. (2012) The Olympics and harm reduction?. Harm reduction journal, 9(1), 33. PMID: 22788912  

  • May 24, 2012
  • 11:15 AM

Clockworks: The Story of Drugs — Part 1

by xylph in xylem || phloem

In this installment, I will discuss why it is difficult to discover, design and develop a drug, in view of our current knowledge of physiology.With numerous, intertwined reactions happening, our body is a complex clockwork of biomachinery gears. What do you do, then, if some gears fail—that is, if you got sick? On one hand, it is a consolation that many gears are what biologists call 'redundant', which means that it's alright that a certain gear fails, because there are other gears that can ta........ Read more »

Welsch, M., Snyder, S., & Stockwell, B. (2010) Privileged scaffolds for library design and drug discovery. Current Opinion in Chemical Biology, 14(3), 347-361. DOI: 10.1016/j.cbpa.2010.02.018  

Marusyk A, Almendro V, & Polyak K. (2012) Intra-tumour heterogeneity: a looking glass for cancer?. Nature reviews. Cancer, 12(5), 323-34. PMID: 22513401  

  • May 20, 2012
  • 03:52 PM

Energy Drinks: What’s the Big Deal?

by Dirk Hanson in Addiction Inbox

The sons of Red Bull are sporting record concentrations of caffeine.
Are energy drinks capable of pushing some people into caffeine-induced psychotic states? Some medical researchers think so, under the right set of conditions.
Red Bull, for all its iconic ferocity, is pretty tame, weighing in at approximately half a cup of coffee. Drinks like Monster Energy and Full Throttle push it up to 100-150, or the equivalent of a full cuppa joe, according to USDA figures at Talk About Coffee. That does........ Read more »

  • April 28, 2012
  • 01:41 AM

Banned antibiotics in feather meal - A discussion with an author of the study

by Austin Bouck in Animal Science Review

Following my recent post where I examined an article from Johns Hopkins that found multiple contaminants in commercial feather meal (including fluoroquinolones, a class of antibiotics that have been banned from use in poultry since 2005), I was honored to be contacted by one of the Authors, Dr. David Love. Dr. Love offered to continue the discussion with me, and was happy to answer my questions regarding the study, the media frenzy it has inspired, and some of the goals of the research conducted........ Read more »

  • April 7, 2012
  • 04:47 AM

A typical QSAR study (cite:citesAsAuthority)

by egonw in Chem-bla-ics

I use CiTO to keep track of how the CDK is cited and used, and just looked at a typical QSAR paper. Here are my comments on "Study of indole derivative inhibitors of Cytosolic phospholipase A2α based on Quantitative Structure Activity Relationship", by Lu et al (doi:10.1016/j.chemolab.2011.11.011). Normally, I am fairly short in these reviews which I publish via the CDK Google+ page, briefly describing what CDK functionality is being used. But this time the post became a more substantial r........ Read more »

  • March 15, 2012
  • 09:31 PM

Caramel Color Carcinogens -- Bring Back Crystal Pepsi Part 2

by DJ Busby in Astronasty

Recently in the news, 4-MEI in cola's caramel coloring includes a carcinogen. I explain the severity, and follow it up with my proposal for the resurrection of Crystal Pepsi.... Read more »

National Toxicology Program (NTP, 2007). (2007) Chemical Meeting The Criteria For Listing As Causing Cancer Via The Authoritative Bodies Mechanism: 4-Methylimidazole. NTP Technical Report Series. info:other/NIH: 07-4471

  • March 8, 2012
  • 07:00 AM

Blood Pressure Pills to Combat Racism: Research

by United Academics in United Academics

Researchers from the Oxford University have found that people consuming a common heart disease drug, propranolol (40 mg), show less implicit racism than those who don’t consume the medicine. The drug acts on the mechanisms that activate fear, which, according to the scientists, is the main cause of racism.... Read more »

Terbeck, S., Kahane, G., McTavish, S., Savulescu, J., Cowen, P., & Hewstone, M. (2012) Propranolol reduces implicit negative racial bias. Psychopharmacology. DOI: 10.1007/s00213-012-2657-5  

  • February 26, 2012
  • 11:40 AM

Friday Roundup-Eating Roadkill and Turtle Troubles in Canada

by David Steen in Living Alongside Wildlife

A New York Snapping Turtle
Protecting Snapping Turtles in Canada.  The distribution and range of a species is often heavily influenced by climate and habitat. If an area does not have suitable climate or habitat for a species, they cannot occur there. It's that simple. Polar Bears would not be comfortable in tropical jungles and you will not find Green Iguanas basking on icecaps. It gets a ... Read more »

Cedervall, T., Hansson, L., Lard, M, Frohm, B, & Linse, S. (2012) Food Chain Transport of Nanoparticles Affects Behaviour and Fat Metabolism in Fish. PLoS ONE, 7(2). info:/

Allender MC, Dreslik M, Wylie S, Phillips C, Wylie DB, Maddox C, Delaney MA, & Kinsel MJ. (2011) Chrysosporium sp. infection in eastern massasauga rattlesnakes. Emerging infectious diseases, 17(12), 2383-4. PMID: 22172594  

  • December 22, 2011
  • 05:42 PM

Unruly beasts in the jungle of molecular modeling

by The Curious Wavefunction in The Curious Wavefunction

The Journal of Computer-Aided Molecular Design is having a smorgasbord of accomplished modelers reflecting upon the state and future of modeling in drug discovery research and I would definitely recommend anyone - and especially experimentalists - interested in the role of modeling to take a look at the articles. Many of the articles are extremely thoughtful and balanced and take a hard look at the lack of rigorous studies and results in the field; if there was ever a need to make journal articl........ Read more »

  • December 13, 2011
  • 10:36 AM

On reproducibility in modeling

by The Curious Wavefunction in The Curious Wavefunction

A recent issue of Science has an article discussing an issue that has been a constant headache for anyone involved with any kind of modeling in drug discovery - the lack of reproducibility in computational science. The author Roger Peng who is a biostatistician at Johns Hopkins talks about modeling standards in general but I think many of his caveats could apply to drug discovery modeling. The problem has been recognized for a few years now but there have been very few concerted efforts to addre........ Read more »

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