The last couple of years have disrupted classes for many students, I helped devise a course for MRes students at UCL undertake a computational drug discovery project using open source tools. A pleasure to work with a group of really bright and enthusiastic group of students

The workflow has now been written up as a Lab Manual which is available for anyone to use.

The publication describing the work is now available (Open Access) Molecular Docking with Open Access Software: Development of an Online Laboratory Handbook and Remote Workflow for Chemistry and Pharmacy Master’s Students to Undertake Computer-Aided Drug Design DOI.

In response to the closure of many university laboratories due to the Covid-19 pandemic in 2020, a handbook and remote webinar approach designed to support students in the use of software tools for computer-aided drug design has been developed. Specifically, the course has been designed for chemistry and pharmacy students who have little or no experience of computational techniques and can use open-source software on their own machines. In this way a flexible and relevant course, giving a rigorous academic experience, could be delivered even in the most challenging of circumstances. We believe that this laboratory protocol will help to “democratize” the scientific process in this field.

The lab Manual is available in a GitHub repository. https://github.com/UCL/OpenDockingLab_Handbook.

This repository is the place to store and edit the lab handbook for UCL teaching courses that involve the use of open source tools in molecular docking.

Files currently available are shown above, on this "code" tab. The most recent version of the lab manual is there, for download and the manual is also available in full on the wiki as a living document that can be updated by anyone, year on year. If you'd like to suggest edits it's easy to do that by opening an Issue (tab above).

We'd love to hear of new docking tools or scoring functions that we could include.

Feel free to contribute.

You might also be interested in the RSC CICAG YouTube channel https://www.youtube.com/c/RSCCICAG that contains many workshops highlighting Open Source tools for Chemistry.

 

A recent publication caught my eye.

Extraction of organic chemistry grammar from unsupervised learning of chemical reactions DOI.

Anyone who has been involved in building a reaction database will know that atom mapping reagents/starting materials onto products is a very time-consuming and tedious process, that is often fraught with errors. So any method that automates this process is a significant step forward.

Here, we demonstrate that Transformer Neural Networks learn atom-mapping information between products and reactants without supervision or human labeling. Using the Transformer attention weights, we build a chemically agnostic, attention-guided reaction mapper and extract coherent chemical grammar from unannotated sets of reactions. Our method shows remarkable performance in terms of accuracy and speed, even for strongly imbalanced and chemically complex reactions with nontrivial atom-mapping. It provides the missing link between data-driven and rule-based approaches for numerous chemical reaction tasks.

They also supply a file containing Common patent reaction templates. This file contains the most common patent reaction templates (USPTO grants), including the year of the first appearance, the patent numbers, frequently used reagents, and the template count. The templates were extracted after applying RXNMapper to generate the atom-mapping.

 

The latest RSC CICAG newsletter (Winter 2020) is now available http://rsccicag.org/newsletters.htm. It includes:-

Chemical Information & Computer Applications Group Chair's Report
CICAG Planned and Proposed Future Meetings
Memories of Dr Angus McDougall, 1934-2020
CASP14: DeepMind’s AlphaFold 2 – an Assessment
Meeting Report: 3rd RSC BMCS & CICAG AI in Chemistry Meeting
ReadMe and HowTo for Lightning Poster Presentations
As Conferences went Online: What do we miss the most?
Alan F Neville, 1943-2020, BSc, PhD
Parallel Processing for Molecular Modeling in ChemDoodle 3D
Catalyst Science Discovery Centre & Museum Trust: A Year in Review
The 6th Tony Kent Strix Annual Memorial Lecture 2020
Open Chemical Science Meetings and Workshops - Introduction
Open Access Publishing for Chemistry – Meeting Reports
Open Data for Chemistry – Meeting Reports
Open Source Tools for Chemistry – Workshop Reports
RSC Open Access Journals and Future Plans
RSC’s Journal Archives Available for Text and Data Mining
Chemical Information / Cheminformatics and Related Books
News from AI3SD 64 Other Chemical Information Related News

 

An interesting free virtual meeting from RSC-CICAG, Full details and registration are here https://www.rsc.org/events/detail/43178/open-access-publishing-for-chemistry.

Scientists, librarians and publishers are all affected by the rapidly changing landscape of open access publishing, the proliferation of options available, and in some cases the confusion and uncertainty which can arise. The implementation of Science Europe's "Plan S", which stipulates that from 2021 scientific publications resulting from research funded by public grants must be published in compliant open access journals or platforms, will be a significant milestone. As well as examining the implications of Plan S in the UK and elsewhere, this meeting will explore the broader impact of open access publishing on the chemical sciences, addressing issues such as open access models, organisations' and end-users' experiences, licensing, ethics, benefits and pitfalls. Use cases illustrating new opportunities provided to chemistry by open publishing will also be presented.

Keynote: Dr Martin Hicks: 'Enabling Open Science'

Contributed talks:

Dr Marshall Brennan: 'ChemRxiv: Year One and beyond'
Rachel Bruce: 'Open access for UK Research and Innovation: emerging policy for 2021'
Clair Castle: 'How open are chemists?'
Dr Neil Hammond: 'Open Access: a society publisher's perspective'
Helen Malone: 'The growth in importance of open access sources in the pharmaceutical industry'
Prof Cameron Neylon: A tale of two societies: Are differences in open access policy driving a split in UK and US chemistry publishing?
Dr Tony Ross-Hellauer: 'Pros and cons of open peer review'
Dr Egon Willighagen: 'Open science in an open access world'

There is also Workshop on Open-Source Tools for Chemistry, and Open Data for Chemistry.

 

Another interesting free virtual meeting from RSC-CICAG on 10 November 2020 16:00 - 12 November 2020

Huge quantities of data are generated in the chemical sciences although frequently these data are behind paywalls or protected intellectual property of organisations. Recently however there has been a tendency for more openness in scientific data in general and specifically the chemical sciences. There is now a large quantity of open data mined from the literature over decades offering new opportunities to learn from these data thereby improving scientific endeavour. However ensuring data accessibility, discovery and quality is still a major issue. The meeting will offer guidance on data curation and wrangling in order to be able to be applied effectively.

Speakers:

Dr Ed Griffen, MedChemica
Dr Kim Jelfs, Imperial College London
Dr Samantha Kanza, University of Southampton
Prof John Overington, Medicines Discovery Catapult
Prof Matthew Todd, University College London
Dr Barbara Zdrazil, University of Vienna

Registration This event will be free to attend but registration is required.

Full details and registration are here https://www.rsc.org/events/detail/43179/open-data-for-chemistry.

This event is part of the Open Chemical Science Week organised by CICAG.

The other events are

Open Access Publishing for Chemistry

Workshop on Open-Source Tools for Chemistry.

 

An interesting free virtual meeting from RSC-CICAG.

Scientists, librarians and publishers are all affected by the rapidly changing landscape of open access publishing, the proliferation of options available, and in some cases the confusion and uncertainty which can arise. The implementation of Science Europe's "Plan S", which stipulates that from 2021 scientific publications resulting from research funded by public grants must be published in compliant open access journals or platforms, will be a significant milestone. As well as examining the implications of Plan S in the UK and elsewhere, this meeting will explore the broader impact of open access publishing on the chemical sciences, addressing issues such as open access models, organisations' and end-users' experiences, licensing, ethics, benefits and pitfalls. Use cases illustrating new opportunities provided to chemistry by open publishing will also be presented.

Keynote: Dr Martin Hicks: 'Enabling Open Science'

Contributed talks:

Dr Marshall Brennan: 'ChemRxiv: Year One and beyond'
Rachel Bruce: 'Open access for UK Research and Innovation: emerging policy for 2021'
Clair Castle: 'How open are chemists?'
Dr Neil Hammond: 'Open Access: a society publisher's perspective'
Helen Malone: 'The growth in importance of open access sources in the pharmaceutical industry'
Prof Cameron Neylon: A tale of two societies: Are differences in open access policy driving a split in UK and US chemistry publishing?
Dr Tony Ross-Hellauer: 'Pros and cons of open peer review'
Dr Egon Willighagen: 'Open science in an open access world'

Full details and registration are here https://www.rsc.org/events/detail/43178/open-access-publishing-for-chemistry.

 

There is currently much discussion about how access to data, information, knowledge and the software tools essential for 21st century chemical science research can be increased and simplified while ensuring that quality is maintained. Significant progress is being made, but the myriad of policies, repositories, standards, sources, tools and subscription models is at the same time complicating the landscape.

To address the many questions concerning the rapidly evolving open research landscape, towards the end of last year (before Covid-19), the CICAG Committee started to plan a series of three one-day events in November 2020, covering open access publishing, open data and open source software. The aim was to examine the benefits, risks and likely future developments and their impact on research. The aim hasn’t changed but, due to Covid-19, the events will now be run as a series of online webinars to take place over five days, from 9-13 November 2020. CICAG have decided to make them free of charge - this has been possible because the cost of running online events is much less than for face-to-face meetings.

For further information and to register see:

• Open Access Publishing: https://www.rsc.org/events/detail/43178/open-access-publishing-for-chemistry
• Open Data: https://www.rsc.org/events/detail/43179/open-data-for-chemistry
• Open Source Software: https://www.rsc.org/events/detail/43180/workshop-on-open-source-tools-for-chemistry

 

The Royal Society of Chemistry’s Chemical Information and Computer Applications Group (CICAG) is organising a series of three one-day events with the theme “Open Chemical Science” on 11-13 November 2020. Venue: RSC, Burlington House, London, United Kingdom To find out more and to register, visit the web pages for the events:

• Open Access Publishing for Chemistry: https://www.rsc.org/events/detail/43178/open-access-publishing-for-chemistry
• Open Data for Chemistry: https://www.rsc.org/events/detail/43179/open-data-for-chemistry
• Workshop on Open-Source Tools for Chemistry: https://www.rsc.org/events/detail/43180/workshop-on-open-source-tools-for-chemistry

Submissions of abstracts for oral or poster presentations are invited for the "Open Access Publishing for Chemistry" and "Open Data for Chemistry" days. The submission forms, information about deadlines and the submission process are on the web pages above. Please contact Gillian Bell, cicageventsmanager@gmail.com, with any enquiries.

A number of bursaries are available to support registration and travel costs for postgraduate students, the retired and those on career breaks. An application form is available on this page and further information regarding travel grants available for RSC members can be found at: www.rsc.org/awards-funding/funding/#funding-options.

* If it is not possible to run the meetings at Burlington House due to Covid-19, they will be held as webinars or online events.

 

This looks like it should be well worth bookmarking.

https://www.biomedcentral.com/collections/programming-languages

This thematic series comprises a set of invited papers, each one describing the use of a single language for the development of cheminformatics software that implement algorithms and analyses and aims to cover a variety of language paradigms. The issue will be rolling, such that as papers on new languages are submitted they will be automatically added to this issue.

The first article DOI is by Kevin Theisen (of ChemDoodle fame) reviewing HTML5/Javascript. Apparently there have been more lines of Javascript written than all other programming languages combined so it seems appropriate as a kick off article.

 

A while back I wrote a very popular page describing how to install a wide variety of chemiformatics packages on a Mac, since there have been some changes with Homebrew which have meant that a few of the scientific applications are no longer available so I've decided to rewrite the page on installing the missing packages using Anaconda.

I've also included a list of quick demos so you can everything is working as expected.

Full details are here

Packages include:

• OpenBabel
• RDKit
• brew install cdk
• chemspot
• indigo
• inchi
• opsin
• osra
• pymol
• oddt

In addition to gfortran and a selection of developers tools.

 

The Chemical Reference Resolver is an invaluable tool for quickly directing you to a publisher's webpage that contains the article you are looking for. However many of the publications are now also available on preprint servers and are accessible for free even if the final publication is behind a paywall.

To search for open access versions simply prepend your doi string with the word "oadoi" and press Enter.

Full details are in this blog post http://kovsky.net/blog/posts/oadoi-resolving.

 

Sci-Hub is a web service that provides free access to research articles and latest research information, the website uses donated library credentials of contributors to circumvent publishers’ paywalls and thus downloads large parts of their collections. In 2016 Sci-Hub released data on ~28 million downloads done through the service and in 2017 Sci-Hub released the list of ~ 62 million Digital Object Identifiers (DOIs) of the content they have stored.

A recent publication DOI describes a detailed analysis of Sci-Hub usage and as you can see in the plot below taken from the article chemistry journals (shown in red) are particularly popular.

 

With Safari 5 one of the most interesting new features is the support for Extensions and there are now many different [extensions availabl(https://safari-extensions.apple.com).

There are a section of extensions that might be of interest to scientists and I've started listing the here.

I've just created a new extension that might be of interest.

Ever come across an interesting paper that is behind a paywall? Many of these publications may also be available via green open access.

Self-archiving, also known as green open access, refers to the practice of depositing articles in an institutional repository or a subject repository such as arXiv.

However locating the open version can be a bit hit and miss given there are so many potential repositories. Fortunately oaDOI provides a simple way to search for open access versions

You can simply paste the DOI into the search engine at oadoi.org, however this web service is ideal for linking to a Safari Extension.

Read more…