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Cambridge MedChem Consulting

Drug Discovery Resources Updated

I've spent a little time updating the Drug Discovery Resources Section of the website. In particular:

halogenbindingcomparison

Molecular Interactions page updated

The Molecular Interactions page has been updated to include a section on anion-aryl interactions.

anion_aryl

Website Update

A couple of people have asked me how to access the category tags that are attached to news items, the short answer is not easily so I've created a new tab at the top of the page that gives you direct access.

newscategories

Click on the link and you will get an alphabetical listing of all categories with appropriate links.

It may take a day or so for the new menu bar to appear on all pages.

Annual Review of website

The Drug Discovery Resources website continues to increase in popularity with over 137,000 page views, an increase of 27% over the figure for 2016. The pages were visited by over 71,000 viewers and around a quarter of the visitors come back on multiple occasions suggesting they find it useful. The visitors come from 177 different countries with the US (31%) and UK (15%) topping the list.

The most viewed pages in 2017 were

There have been a number of significant updates to the Drug Discovery Resources this year, in particular Target Validation has been expanded and the section on Chemical Probes given a separate page, highlighting invaluable resources like Probe Miner. Another new addition to the site has been the page on Covalent Inhibitors I got a significant amount of feedback on this page and it was updated several times.

I posted a poll on the website asking how many molecules are usually selected from a virtual screening run?

screening

Some people also emailed me with further information. For companies with large internal physical screening collections, and the ability to cherry pick samples, it effectively costs the same to fill a high density plate (>1000 compounds) as it does to select a handful of compounds. On the other hand if the scientist has to purchase compounds then the logistics and cost become a significant obstacle.

There have been a couple of publications this year describing problems arising from analysis of high-throughput screening data, I've updated the Analysis of high-throughput screening data page to try and highlight some of the issues and strategies.

One of the highlights of the year for me was the 19th RSC / SCI Medicinal Chemistry Symposium (#19thCamMedChem) which took place 10th-13th September 2017 at Churchill College, Cambridge, UK. In particular a session on Neglected and Tropical Diseases, to increase the exposure of the brilliant science undertaken in this important therapeutic area the conference organisers arranged for this to be a live webinar. The session was also recorded and is now available online.

https://youtu.be/XLOCFrjrMEY

This is a recording of the Neglected and Tropical Diseases Session at the 19th Cambridge MedChem Meeting, 11-13 September 2017. The speakers are Kelly Chibale (Univ of Capetown), Christoph Boss (Actelion), Rob Young (GlaxoSmithKline), Jonathan Large (LifeArc) and Charles Mowbray (DNDI). To date this has been watched nearly 250 times.

Please feel free to share. #19thCamMedChem.

The European Lead Factory (ELF) is a collaborative public-private partnership aiming to deliver novel lead molecules for drug discovery programs. When the consortium was formed around 5 years ago there was a lot of scepticism about whether a group of 30 partners rating from large Pharma companies to small academic groups could ever agree on a legal framework that would allow the ELF to function. In a addition, in an industry where confidentiality was critical to maintaining intellectual property the idea that a group of large Pharma companies would share their sample collections often regarded as the "Crown Jewels" seemed impossible. However I was at the European Lead factory Stakeholder Meeting (24-25 April 2017) and it is clear that is has been a success and I've written a summary here.

Interestingly the Books and Grant funding research have seasonal peaks in viewing.

The website was also updated this year to use https rather than http, this involved editing a fair number of of hardcoded URLs. Whilst I don't require any secure transactions it does seem that https offers a level of trust that is beneficial. It seems likely that other web browsers will follow Google's lead and have a popup message when accessing any page using http, I suspect this could rapidly become irritating so I've decided to make the move. You will still able to access using http but I'll be setting up redirects later this week. Hopefully the visitors will not really notice any difference.

Looking at the operating systems 52% are Windows users, 21% Mac users, 10% iOS and 9% Android, Chrome dominates the browser stats (62%) with Safari second (20%) and Firefox third (12%).

Seasons Greetings

IMG_2224

Clare College view of bridge from Old Court

As in previous years all monies saved for not sending greetings cards will be given to the Multiple Sclerosis Society

Causes of death over 100 years

The UK Office of National Statistics has produced a fascinating interactive plot of the causes of death in the UK over the last 100 years.

I've captured a screenshot of the plots but I'd urge to go and have a look at the interactive plot on the website http://visual.ons.gov.uk/causes-of-death-over-100-years/.

deaths

What is very apparent is the impact the introduction of antibiotics had in the late 1940's, and the introduction of mass vaccinations, deaths due to infections have been virtually eliminated.

In men heart disease remains the major killer whilst in women it is breast cancer. Sadly among the young it looks like mental health issues are a major concern.

Website update

I've spent the weekend updating the website to use https rather than http, this involved editing a fair number of of hardcoded URLs. Whilst I don't require any secure transactions it does seem that https offers a level of trust that is beneficial. It seems likely that other web browsers will follow Google's lead and have a popup message when accessing any page using http, I suspect this could rapidly become irritating so I've decided to make the move. You will still able to access using http but I'll be setting up redirects later this week. Hopefully the visitors will not really notice any difference.

secure

If you want to edit your bookmarks here is the new link https://www.cambridgemedchemconsulting.com

Drug Discovery Resources Site Update

I've completed a few updates to the Drug Discovery Resources website, this includes fixing any broken links that people have mentioned to me, and also starting a new section in the Pre-clinical toxicity on Mutagenicity.

Annual Site review

As 2016 ends I'd like to take the chance to wish you all a Happy New Year and hope for great success in your drug discovery endeavours.

This website continues to increase in popularity with over 108,000 page views, an increase of 16% over the figure for 2015. The pages were visited by over 50,000 viewers and around a quarter of the visitors come back on multiple occasions suggesting they find it useful. The visitors come from 160 different countries with the US and UK topping the list.

The most viewed pages were

Interestingly the Books and Grant funding research have seasonal peaks in viewing.

Looking at the operating systems 57% are Windows users, 22% Mac users, 10% iOS and 8% Android, Chrome dominates the browser stats (58%) with Safari second (20%) and Firefox third (15%).

Seasons Greetings

MerryChristmas

As in previous years all monies saved for not sending greetings cards will be given to the Multiple Sclerosis Society

Web browsers used in Drug Discovery

Last week I posted this observation

More and more of the companies/groups that I'm working with are moving away from desktop applications to providing a web-based portfolio of applications for drug discovery. Most seem to use a combination of commercial tools with a selection of in house apps. Whilst this has many advantages it does raise the question about which web browser should they support? Whilst NetMarketshare still has Internet Explorer at 44% this is probably not a good metric to measure browser usage in the Drug Discovery Sector. So for the last couple of months I've been monitoring the web browsers used to access the Drug Discovery Resources since it is unlikely that anyone not interested in drug discovery would spend much time browsing these pages. The results are interesting.

The ranking since 1 Jan 2016 to date is

  1. Chrome 55%
  2. Safari 20%
  3. Firefox 16%
  4. Internet Explorer 4%

Looking at operating systems

  1. Windows 57%
  2. Macintosh 23%
  3. iOS 11%
  4. Android 8%

So the lack users of Internet Explorer is not due to the absence of Windows users. This must have implications for all developers, the users appeared to have moved to the more modern web browsers.

Update

I've now data from around 10 different sites involved in drug discovery or software/databases to support drug discovery, ranging from small sites with about 10,000 hits a month to major sites with many millions of hits a month, and I've now included the average data in the table below.

webbrowsers

It looks like the data from Drug Discovery Resources reasonably reflects the usage in the Drug Discovery sector.

Web-based tools

More and more of the companies/groups that I'm working with are moving away from desktop applications to providing a web-based portfolio of applications for drug discovery. Most seem to use a combination of commercial tools with a selection of in house apps. Whilst this has many advantages it does raise the question about which web browser should they support? Whilst NetMarketshare still has Internet Explorer at 44% this is probably not a good metric to measure browser usage in the Drug Discovery Sector.

So for the last couple of months I've been monitoring the web browsers used to access the Drug Discovery Resources since it is unlikely that anyone not interested in drug discovery would spend much time browsing these pages. The results are interesting.

The ranking since 1 Jan 2016 to date is

  1. Chrome 56%
  2. Safari 20%
  3. Firefox 16%
  4. Internet Explorer 4%

Looking at operating systems

  1. Windows 57%
  2. Macintosh 23%
  3. iOS 11%
  4. Android 8%

So the lack users of Internet Explorer is not due to the absence of Windows users. This must have implications for all developers, the users appeared to have moved to the more modern web browsers.

Update

A number of readers/companies have contacted me since I published with broadly similar results, I hope to compile and publish the anonymised results next week.

Annual Site Review

As 2015 ends I'd like to take the chance to wish you all a Happy New Year and hope for great success in your drug discovery endeavours.

The website increases in popularity with 93,000 page views in 2015 an increase of 24% over last year. Nearly 25% of the visitors come back on multiple occasions which I hope means people are finding the content useful.

Nine of the top ten most popular pages were from the Drug Discovery Resources Pages which I am delighted to see, since it suggests that the work entailed in putting the resources together is worthwhile.

The most viewed pages were

As might be expected the Books page only seems popular coming up to Christmas ;-)

The visitors come from over 100 different countries with US and UK topping the list. Whilst desktop systems predominate nearly 20% now access the site from a mobile device.

Annual Site Review

At the end of each year I take the opportunity to look at the website analytics to see what parts of the website are the most popular. Overall there was a 15% increase in the number of page views up to 75,000. Average time on a page was 2 mins suggesting the content is engaging with the viewers.

Nine of the top ten most popular pages were from the Drug Discovery Resources Pages which I am delighted to see, since it suggests that the work entailed in putting the resources together is worthwhile.

The most viewed pages were

Drug Discovery Resources website updated

I’m in the process of updating the Drug Discovery Resources pages, in particular I’ve updated the Grant Funding resources and Fragment screening.

Drug Discovery Resources website annual report

The Drug Discovery Resources section of the website is intended to act as a resource for scientists undertaking drug discovery, it was originally simply a web page version of a course I used to give but has been continuously expanded and updated. Since this takes a far amount of time I like to monitor usage to check that it is being used.

In 2013 the Drug Discovery Resources section was viewed by nearly 24,000 unique visitors (there were 9000 unique visitors in 2012), 27% of which made more than one visit. There were 65,000 page views and on average visitors viewed two pages per visit. There were visitors from 141 different countries with the US and UK being the most common.

The most frequently accessed pages were

Drug Discovery Resources
Plasma Protein Binding and Distribution
Molecular Interactions
Formulation
Fragment Screening

The most popular sections were

ADME
Bioisosteres
Hit Identification

The top search queries were

Plasma Protein Binding
LogD
Bioisosteres
ADME
Aldehyde Oxidase

Website Update

I’ve now finished updating the website. I’ve changed the host, redesigned the theme and updated almost every page.

Feel free to have a look around and let me know of any issues or suggestios.