Category Archive: Open Data

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 …

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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 …

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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 …

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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 …

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Dec
28

2015 in review

2015 saw the continuation of some research themes from 2014, namely some work on Ebola, rare diseases and Bayesian models for neglected diseases. At the end of the year several papers are in press for next year so more to come. As usual there were some ups and downs in getting some of these to see …

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Aug
20

ACS 2015, chemistry talks, posters and Tattoo!

I am just back from a very busy trip to Boston for the ACS. It was great to meet up with many people I see only rarely, at these meetings as well as meet new people including one with a molecule tattoo that got a lot of interest on Twitter . I gave 5 talks …

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May
28

Turning points and games with a purpose

Today I was talking to one of my old mentors from my postdoc days (in big pharma), for the first time in a few years. I realized that working with him and exposure to computational chemistry software  was a real turning point in my career in 1996. Several more turning points later …and I am …

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May
22

Open Source Bayesian Models (X2)

For the last 5-6 years I have been kind of obsessed (in a good way) with how perhaps we could try to get computational machine learning models for drug discovery to a point where they could be shared. The reasoning behind this being that we publish papers, but the models described in them never really …

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Oct
08

Where is the big Pharma Knight riding in to slay Ebola?

In full disclosure my better half works for a big pharma, this is not going to hold me back from writing what I am sure everyone is thinking. It saddens me as someone who worked for big pharma (until 2001) to have to write this. We are months into the rapidly escalating catastrophe that is …

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Oct
02

A pharmacophore for compounds active against Ebola

I was looking through Pubmed yesterday looking for repurposing efforts applied to Ebola and found the paper by Madrid et al. This described many hits, including chloroquine and amodiaquine. Then I was tweeting with@DokteCoffee last night and she suggested another paper by Johansen et al., which described SERMs such as clomifene and  toremifene. Interestingly Madrid …

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