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  • May 8, 2017
  • 06:45 PM

Let those who never smelled bad cast the first stone

by Aurametrix team in Aurametrix Blog

Analysis of our metabolism is crucial to comprehending the responses of our genes and microbes to the stresses of daily life, and to elucidating the causes and consequences of health and disease. And measurement of urinary metabolites - small molecules produced from foods, drinks, drugs, environmental contaminants, bodily waste products and bacterial by-products - is key to the analysis. We applied this approach to an elusive condition that has always evaded diagnosis: s........ Read more »

Bouatra, S., Aziat, F., Mandal, R., Guo, A., Wilson, M., Knox, C., Bjorndahl, T., Krishnamurthy, R., Saleem, F., Liu, P.... (2013) The Human Urine Metabolome. PLoS ONE, 8(9). DOI: 10.1371/journal.pone.0073076  

Irene S. Gabashvili. (2017) Raw Data from Clinical Trial NCT02692495. Mendeley Data. info:/DOI: 10.17632/8bk6h6bmkr.1

  • February 21, 2014
  • 05:43 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  

  • October 20, 2013
  • 11:07 AM
  • 1,059 views calls for help

by egonw in Chem-bla-ics

I don't think I mentioned this JISC project by David Shotton et al. yet, and should perhaps have done so earlier. But it is not too late, as Shotton is calling out for help in a Nature Comment this week (doi:10.1038/502295a). Now, I have been tracking what is citing the CDK literature using CiteUlike since 2010, and just asked the project developers how I can contribute this data.

Interestingly, the visualization from is interesting as it also shows papers citing papers t........ Read more »

D. Shotton. (2013) Publishing: Open citations. Nature, 502(7471), 295-297. info:/10.1038/502295a

  • June 7, 2013
  • 11:25 AM

Twist, Baby, Yeah Twist

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

If you were born in the 1960′s and if you happen to do The Twist with your partner your heart would of course be racing! Thanks to G protein-coupled inwardly-rectifying potassium channels (GIRKs) your heart can beat back to normal levels. Ironically, the protein does a “twist” to slow down the heart. Go Figure!

GIRK is basically a potassium ion-transporter and found in cardiac cells. It regulates the membrane voltage after the GPCR activated G-beta and G-gamma bind to the tr........ Read more »

  • April 16, 2013
  • 08:15 PM

Say Smiles

by Ragothamanyennamalli in Getting to know Structural Bioinformatics

Recently, Babel (in my system) was not working and I needed to convert my .sdf files to smiles format. I troubleshooted the error was able to run successfully. But, this made me think, what about a web-based application to do this format conversion? That's how I found these three amazing tools based at the National Cancer Institute's CADD Chemoinformatics group.... Read more »

  • April 10, 2013
  • 10:31 AM

Video Tip of the Week: Introductory Cheminformatics

by Mary in OpenHelix

This week’s tip of the week is a bit afield from what we usually cover. But sometimes I see that people are looking for cheminformatics materials from our site, and this resource that I learned about recently seems like a terrific effort to wrangle some of the basics and foundations of cheminformatics (or, as David [...]... Read more »

Wild, D. (2009) Grand challenges for cheminformatics. Journal of Cheminformatics, 1(1), 1. DOI: 10.1186/1758-2946-1-1  

  • January 22, 2013
  • 05:09 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  

  • November 18, 2012
  • 04:39 PM

DHSs and histone modifications: methylation, acetylation, citrullination, and phosphorylation

by egonw in Chem-bla-ics

One day on, and still struggling with the chemistry behind gene regulation. Let no biologist ever tell me again not to use acronyms (yes, I am looking at you!). But it is interesting. I learned a lot about ChIP, histone modifications, etc, etc. This is an amazing world, where specific histone complex protein residues get methylated, acetylated, citrullinated, and phosphorylated. Of course, all this is in the context of the ENCODE meeting we have tomorrow at BiGCaT, where I will try to ........ Read more »

Thurman, R., Rynes, E., Humbert, R., Vierstra, J., Maurano, M., Haugen, E., Sheffield, N., Stergachis, A., Wang, H., Vernot, B.... (2012) The accessible chromatin landscape of the human genome. Nature, 489(7414), 75-82. DOI: 10.1038/nature11232  

Felsenfeld G, Boyes J, Chung J, Clark D, & Studitsky V. (1996) Chromatin structure and gene expression. Proceedings of the National Academy of Sciences of the United States of America, 93(18), 9384-8. PMID: 8790338  

  • November 17, 2012
  • 01:02 PM

The chemistry of DNA modifications for gene regulation

by egonw in Chem-bla-ics

I have started learning about epigenetics, and particularly the regulatory effects of DNA methylation and acetylation. It's cool, it's hot, it's everything we hope will explain genetics, because genes certainly did not.

The chemistry behind this involves interesting pathways, involves storage of information that passes from one generation to another... epigenetic effects down to the grandchild generation have repeatedly been shown now. I likely candidate are mRNAs that persist beyond the cell d........ Read more »

  • September 22, 2012
  • 12:02 PM

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  

  • May 1, 2012
  • 08:20 AM

Why do old books smell? [video]

by GrrlScientist in Maniraptora

SUMMARY: That old book smell brings back so many memories, but what creates that smell? ... Read more »

Strlič, M., Thomas, J., Trafela, T., Cséfalvayová, L., Kralj Cigić, I., Kolar, J., & Cassar, M. (2009) Material Degradomics: On the Smell of Old Books. . Analytical Chemistry, 81(20), 8617-8622. DOI: 10.1021/ac9016049  

  • April 7, 2012
  • 05:47 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 30, 2012
  • 05:36 AM

Researchers One Step Closer to Giving Robots the Ability to “Feel”

by Jason Carr in Wired Cosmos

A particular area of interest I have is the the use of robots in space exploration so I try to keep an eye out for interesting developments within the robotics field to share with you guys. I came across a recently released research paper dealing with mechanical stimuli and thought this might be of interest to [...]... Read more »

  • January 27, 2012
  • 11:00 AM

Watermarking molecules

by Aaron Sterling in Nanoexplanations

I’ve posted twice about Anonymous hacking into Stratfor — and, more generally, their hacktivism has been making bigger and bigger waves.  CNN recently ran a fairly positive story on the support hacktivists are providing the Occupy movement.  Many of these … Continue reading →... Read more »

Joachim J. Eggers, W.D. Ihlenfeldt, & Bern Girod. (2001) Digital Watermarking of Chemical Structure Sets. Information Hiding, 200-214. DOI: 10.1007/3-540-45496-9_15  

  • December 7, 2011
  • 09:50 PM

Why drug design is like airplane design. And why it isn't.

by The Curious Wavefunction in The Curious Wavefunction

Air travel constitutes the safest mode of travel in the world today. What is even more impressive is the way airplanes are designed by modeling and simulation, sometimes before the actual prototype is built. In fact simulation has been a mainstay in the aeronautical industry for a long time and what seems like a tremendously complex interaction of metal, plastic and the unpredictable movements of air flow can now be reasonably captured in a computer model.In a recent paper, Walter Woltosz of Sim........ Read more »

  • October 18, 2011
  • 05:53 AM

The Blue Obelisk Shoulders for Translational Cheminformatics

by egonw in Chem-bla-ics

I guess reader of my blog already heard about it via other channels (e.g. via Noel's blog post), but our second Blue Obelisk paper is out. In the past five-ish years since Peter instantiated this initiative, it has created a solid set of shoulder on which to developed Open Source-based cheminformatics solutions. I created the following diagram for the paper, showing how various Blue Obelisk projects interoperate (image is CC-BY, from the paper):

It shows a number of Open Standards (diamonds)........ Read more »

Guha, R., Howard, M., Hutchison, G., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J., & Willighagen, E. (2006) The Blue ObeliskInteroperability in Chemical Informatics. Journal of Chemical Information and Modeling, 46(3), 991-998. DOI: 10.1021/ci050400b  

O'Boyle NM, Guha R, Willighagen EL, Adams SE, Alvarsson J, Bradley JC, Filippov IV, Hanson RM, Hanwell MD, Hutchison GR.... (2011) Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on. Journal of cheminformatics, 3(1), 37. PMID: 21999342  

  • October 11, 2011
  • 09:49 PM

GPCR modeling: The devil hasn't left the details

by The Curious Wavefunction in The Curious Wavefunction

The last decade has been a bonanza decade for the elucidation of structures of G Protein-Coupled Receptors (GPCRs), culminating with the landmark structure of the first GPCR-G protein complex published a few weeks ago. With 30% of all drugs targeting these proteins and their involvement in virtually every key aspect of health and disease, GPCRs remain glowingly important targets for pure and applied science.Yet there are miles to go before we sleep. Although we now have more than a dozen structu........ Read more »

Carlsson, J., Coleman, R., Setola, V., Irwin, J., Fan, H., Schlessinger, A., Sali, A., Roth, B., & Shoichet, B. (2011) Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nature Chemical Biology. DOI: 10.1038/nchembio.662  

  • October 9, 2011
  • 03:46 AM

An ontology for QSAR and cheminformatics

by egonw in Chem-bla-ics

QSAR and QSPR are the fields that statistically correlate chemical substance features with (biological) activities (QSAR) or properties (QSPR). The chemical substance can be molecular structures, drug (which are not uncommonly mixtures), and true mixture like nanomaterials (NanoQSAR). Readers of this blog know I have been working towards making these kind of studies more reproducible for many years now.

Parts of this full story include the Blue Obelisk Data Repository (BODR), QSAR-ML, the CDK f........ Read more »

  • July 13, 2011
  • 07:58 AM

CDK Forks

by egonw in Chem-bla-ics

Forking is an important part of Open Source development, and forking is good. Of course, forks should interact too, and genes from one fork should merge back into another fork. Forks are probably also a good indication for the success of a project: if a project is forked, it means it is significant. On the other hand, it can also mean that the main project is too hard to work with. Maybe the CDK is that. Indeed, it's easier to not have your code peer-reviewed, and just fork. That is freedom. (........ Read more »

  • June 17, 2011
  • 05:03 PM

Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions

by egonw in Chem-bla-ics

I was recently asked about a volume descriptor in Bioclipse, which is not yet available. Jmol can calculate surfaces, so that was my first thought. However, I then ran into a paper from 2003 by Zhao, called Fast Calculation of van der Waals Volume as a Sum of Atomic and Bond Contributions and Its Application to Drug Compounds (doi:10.1021/jo034808o).

The paper presents a very simple mathematical model, which approximates the molecular volume by a sum of atomic contributions, and a three terms t........ Read more »

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