Category Archive: open notebook science

Feb
19

Zika Virus- insights from old papers when you can get them

Hunting for information on the Zika virus has revealed several insights for me, both of them point to areas that are obvious. 1. Researchers may have missed out by not reading anything older than a few years old and 2. for all the pronouncements on data sharing and open access, still publishers have not opened …

Continue reading »

Feb
16

An illustration of the virus and summary of Research Priorities to Inform Public Health and Medical Practice for Domestic Zika Virus: A Workshop

Late last week I was contacted by John Liebler a science and medicine illustrator and he had seen the Zika glycoprotein E homology model and wanted to use it to produce an image of the virus.  After reading up on flaviviruses it appeared to me that the original model was of the trimer and not …

Continue reading »

Feb
11

A passion for Zika: does anyone want to find an antiviral?

What gets your heart beating fast? For some it is making science progress as fast as they can because life is too short. For me it gets into something totally new and seeing how quickly you can contribute and collaborate with others. How fast can we bring scientists together to do something? I would argue …

Continue reading »

Feb
03

A Zika drug discovery collaboration

Today a nice collaboration has lead to submission of an opinion article to F1000Research. As an experiment I have posted the manuscript and some of the supplemental data online at FigShare. I hope to add more as time permits. This is definitely a work in progress. This project has consumed lots of time from all …

Continue reading »

Jan
29

Zika Virus – getting some research moving on drug discovery

Following my last post / plea I have been a little preoccupied trying to find scientists that could : 1. contribute to an open Zika virus drug discovery effort 2. Help write a perspective that summarizes potential drug discovery efforts . Fortunately several folks connected by email or twitter to offer ideas and assistance. I …

Continue reading »

Jan
21

Lets do it all again updating predictions for the ‘real’ BIA 10-2474

After todays unmasking of the ‘real’ BIA 10-2474 I ran it through some of the online tools used earlier and now I have found software issues – that darn pyridine 1 -oxide is not liked by some of the websites probably because they use the same SMILES to structure software plugin? SwissTarget Prediction identifies FAAH1 …

Continue reading »

Jan
21

is the structure of BIA 10-2474 actually BIA 10-2474

Well the protocol released by Bial for the clinical trial lists a molecule 3-(1-(cyclohexyl(methyl)carbamoyl)-1H-imidazol-4-yl)pyridine 1-oxide that when run through online software to convert it looks nothing like the one used previously and posted on wikipedia etc. I used 2 websites to convert name to structure Opsin and Openmolecules.org This looks like a puzzle that could …

Continue reading »

Jan
21

Differences between similar FAAH inhibitors and their in silico target predictions

**UPDATE As of 21st Jan 2016 please note the actual structure of BIA 10-2474 changed to this. The continuing follow up to the clinical trial disaster. Chris Southan yesterday suggested I try CID 57880883 as the comparator to CID 54576693 (JNJ-42165279).  These have IC50 75 nM vs 350 nM, respectively according to Jannsen’s WO2011139951. Yesterday …

Continue reading »

Jan
20

BIA 10-2474 is not that similar to synthetic cannabinoids and comparison to another FAAH compound

**UPDATE As of 21st Jan 2016 please note the actual structure of BIA 10-2474 changed to this. Lauren commented on an earlier post about synthetic cannabinoid toxicities and stroke potential. I took the structure of BIA 10-2474 and looked at the similarity to  a virtual library of synthetic cannabinoids which Matthew Krasowski and I had …

Continue reading »

Jan
19

Using more online software to make predictions for BIA 10-2474

**UPDATE As of 21st Jan 2016 please note the actual structure of BIA 10-2474 changed to this.   To continue the theme of the last few posts on the BIA 10-2474 compound in which I have used over 2000 Bayesian models and an App as well as another groups target prediction tool. To take this …

Continue reading »

Older posts «