Category Archive: data quality

Dec
20

Small Molecule Bioactivity Databases Book Chapter

Its been a busy year transitioning from spending most of my time with CDD to my start-up Collaborations Pharmaceuticals, Inc etc. Along the way I found time to write a few book chapters. One of these recently published in High Throughput Screening Methods : Evolution and Refinement Editors: Joshua A Bittker, Nathan T Ross Our …

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Jan
20

Where will BIA 10-2474 lead us?

**UPDATE As of 21st Jan 2016 please note the actual structure of BIA 10-2474 changed to this. My “Armchair science” / speculative contributions on this blog for the clinical trial disaster with BIA 10-2474 got a bit of notice over the past few days at Forbes and C&E News. There have also been discussions with …

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Jan
18

BIA 10-2474 – more predictions

**UPDATE As of 21st Jan 2016 please note the actual structure of BIA 10-2474 changed to this.   I thought it perhaps worth trying other computational approaches with BIA 10-2474. First up is the similarity ensemble analysis (SEA)  from the Shoichet lab. This also makes use of ChEMBL (version 16 data). This seems to agree …

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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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Nov
20

Sanofi and AZ share 210,000 compounds -can we go further?

In the Wall Street Journal today (section B), nestled under an article on Star Wars aim to be a Box -office behemoth, was a small article by Denise Roland on drug giants. This described  the news that AstraZeneca and Sanofi announced  they will each share 210,000 of their compounds from their 2-3 million libraries. This …

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Jul
21

Wiki, Wiki, Wiki – for chemical probes

Sorry for the cheap title (for those born after the mid 80’s its a reference to a song by a funk band called Newcleus). A very interesting commentary published today in Nature Chemical Biology by Arrowsmith et al and its all about chemical probes. Go check it out and note that it took over 50 …

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Mar
22

What warrants an erratum and why the old publishing model must change

Friday AM my day started with an email which I have marked up and added links to Dear Dr. Ekins: It has come to our attention that an error was identified in your recent Perspective entitled “The parallel worlds of public and commercial bioactive chemistry data” published in the March 12, 2015 issue of the …

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Dec
15

A year in publications – 2014

A year in collaborative publications, the ups and downs and a few random comments as well (with a big thanks to all involved): 1. Ekins S and Freundlich JS and Coffee M, A common feature pharmacophore for FDA-approved drugs inhibiting the Ebola virus, F1000research, 3: 277, 2014. This came initially from a Twitter exchange of …

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Dec
04

Chemical probes and parallel database worlds – who wants to know? More publishing fun

    This post is long and a highly detailed description of the challenges involved in getting scientific work published on one level, on another it gets to the heart of discoverability of data, data analysis and just the slog of publishing something that you hope is going to interest others in your direct field. …

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May
01

1 year ago today..I published in PLOS ONE

Today marks the anniversary of my first paper in PLOS ONE with Joe Olechno and Antony Williams (Dispensing Processes Impact Apparent Biological Activity as Determined by Computational and Statistical Analyses). This was quite an event probably for all the wrong reasons in that the evolution of the paper was shaped by rejection after rejection elsewhere …

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