The latest RSC CICAG newsletter is now available http://www.rsccicag.org/indexhtmfiles/CICAG%20Newsletter%20Winter%202022-23%20FINAL.pdf.

This is a really bumper issue

Contents Chemical Information and Computer Applications Group Chair’s Report
CICAG Planned and Proposed Future Meetings
Social Media Migration – Opening up Mastodon as a Tool for Scholarly Communication
Cheminformatics: A Digital History ‒ Part 2. A Personal Perspective of the Role of the Web During the Period 1993-1996
InChI Technical Developments
Update from the Royal Society of Chemistry Library
The Open Free Energy Project
Meeting Report: SCI-RSC Workshop on Computational Tools for Drug Discovery 2022
A Crystallography Papermill: The CSD Response
Meeting Report: Ultra-Large Chemical Libraries
Open Science in the Royal Society of Chemistry
The Davy Notebooks Project
This JACS Does Not Exist: Generating Chemistry Abstracts with Machine Learning
Meeting Report: RSC-CICAG and RSC-BMCS 5th Artificial Intelligence in Chemistry Conference.
EU-OPENSCREEN ERIC: an Open-access Research Infrastructure for Chemical Biology and Early Drug Discovery
DECIMER ‒ An Open Toolkit for Optical Chemical Structure Recognition and Document Analysis
Cryo-EM for Industrial-Scale Structure-Based Drug Design
Cryo-EM & Drug Discovery
2022 CSD Updates
News from ACS CINF
News from CAS
RSC Databases Update
UKeiG: Winners of the Prestigious Tony Kent Strix Award 2022
AI4SD News
Book Review: Digital Transformation: New Tools and Methods for Mining Technological Intelligence
Cheminformatics and Chemical Information Books
2022 Reflections on Life at the Catalyst Science and Discovery Centre and Museum in Widnes
Other Chemical Information News

Contributions to the CICAG Newsletter are welcome from all sources ‒ please send to the Newsletter Editor Dr Helen Cooke FRSC: email helen.cooke100@gmail.com

When you renew your Royal Society of Chemistry membership you can choose “Chemical Information and Computer Applications Group” (group 86) as one of your groups to be a member of. Use the “Connecting with others” button at https://members.rsc.org/ If you have already submitted your form you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141)

The lineup for the 5th Artificial Intelligence in Chemistry Symposium (Thursday-Friday, 1st-2nd September 2022) is now complete for both oral and poster presentations. It really is a fantastic selection of topics and speakers and it is clear this event is now a highlight of the scientific calendar.

The details are here https://www.rscbmcs.org/events/aichem22/

Registration is now open, register here https://www.eventsforce.net/hg3/221/home. In person registration deadline: Monday 29th August 17:00 (BST)

The RSC CICAG newsletter is now available

http://www.rsccicag.org/indexhtmfiles/CICAG%20Newsletter%20Summer%202022%20FINAL pdf

Chemical Information and Computer Applications Group Chair’s Report 4
Your CICAG Committee - Introducing Our New Members 5
CICAG Planned and Proposed Future Meetings 6
Free Workshops on Open-Source Tools for Chemistry 7
The COVID Moonshot 7
Practical Cheminformatics with Open-Source Software 11
The Catalyst Science and Discovery Centre Archives 12
Chemical Data Recovery 3: Legacy Chemical Data Recovery 15
Svante Wold, 1941-2022 22
Cheminformatics: a Digital History - Part 1 Early days at Sheffield: a Personal Perspective 23
Being #CompChemURG: Forging New pathways 28
UKeiG Call for Nominations for the Prestigious Tony Kent Strix Award 2022 29
Welcome to the New Era of Scientific Publishing 30
Greg Landrum Receives the Mike Lynch Award 37
Bioinformatics in the Post-AlphaFold 2 Era 38
Diana Leitch – Reflections on her Life in Chemistry, Chemical Information and Librarianship 45
Meeting Report: AI in Drug Discovery 50
AI4SD News 53
The IUPAC Green Book 55
RSC Historical Group – Women in Chemistry Symposium 56
ACS CINF Report for July 2022 57
News from CAS 57
Chemical Information / Cheminformatics and Related Books 59
Other Chemical Information News 61

We have already started compiling content for the winter newsletter, if you have suggestions or would like to contribute please get in touch.

 

The latest of the RSC CICAG workshops is now online https://youtu.be/Ka08REoGYvI.

The is the latest in 20 workshops that are available on the RSC CICAG YouTube channel https://www.youtube.com/c/RSCCICAG. These workshops have now been viewed over 21,000 times and they are a fabulous way to find out about some of the Open-Source tools and resources that are available to chemists.

RSC CICAG are also organising a number of meetings

Details of the RSC CICAG meeting on Ultra-large Chemical Libraries are available on the CICAG website http://www.rsccicag.org/ultra-large%20chemical%20libraries.htm.

This one-day meeting will be held on 10 August 2022 10:00-17:00, at Burlington House, London. Registration is open https://www.rsc.org/events/detail/73675/ultra-large-chemical-libraries the speakers have been finalised and looks a great line-up. Remember bursaries are also available.

RSC CICAG and BMCS are organising the 5th Artificial Intelligence in Chemistry Symposium. #AIChem22

This two day meeting (Thursday-Friday, 1st-2nd September 2022) will be held at Churchill College Cambridge UK. Details of the meeting and registration are on the conference page website https://www.rscbmcs.org/events/aichem22/.

RSC CICAG in collaboration with the SCI are also organising the SCI-RSC Workshop on Computational Tools for Drug Discovery 2022.

This will be held on 23 November 2022 at The Studio Birmingham. Full details and registration are on the website https://www.soci.org/events/fine-chemicals-group/2022/scirsc-workshop-on-computational-tools-for-drug-discovery-2022

 

The latest RSC CICAG Open-Source Tools for Chemistry workshop

23 June 2022 Scoring of shape and ESP similarity (Ester Heid)

Electrostatic effects along with volume restrictions play a major role in enzyme and receptor recognition. Evaluating electrostatic and shape similarities of pairs of molecules such as proposed versus known ligands can therefore be valuable indicators of prospective binding affinities. This workshop will demonstrate how to compute electrostatic and shape similarities using the open-source tool ESP-Sim github.com/hesther/espsim, doi.org/10.26434/chemrxiv-2021-sqvv9-v3. Available options for comparing electrostatics will be discussed interactively on selected examples of public datasets, along with advice on embedding and aligning molecules prior to computing similarities.

Whilst comparing molecules using 1D or 2D descriptors is well known, most molecules are three dimensional, as are biomolecule binding sites. The comparison of molecular shapes and electrostatics is particularly challenging and this workshop is a perfect introduction. Come along and you have a chance to ask questions directly.

Registration

https://www.eventbrite.com/e/open-source-tools-for-chemistry-tickets-294585512197?.

 

More details of the RSC CICAG meeting on Ultra-large Chemical Libraries are available.

This one-day meeting will be held on 10 August 2022 10:00-17:00, at Burlington House, London.

Registration is open https://www.rsc.org/events/detail/73675/ultra-large-chemical-libraries and a number of the speakers have been finalised and looks a great line-up.

Roger Sayle, NextMove Software Limited, United Kingdom
Carol Mulrooney, GSK, United States
Jan H Jensen, University of Copenhagen, Denmark
Noah Harrison, Evariste Technologies, United Kingdom
Peter Pogany, GSK, United Kingdom

There is still time to submit poster abstracts. A limited number of bursaries are available, the application form should be submitted to the organisers. A maximum of £300 will be reimbursed on submission of receipts.

If you would like to exhibit, sponsor or support this meeting please contact the organisers.

This meeting is supported by

 

Update on the next RSC CICAG Open Source Tools for Chemistry workshops

PDBe Knowledge Base

This workshop explores the Protein Data Bank in Europe Knowledge Base (PDBe-KB https://www.ebi.ac.uk/pdbe/) resource and its tools for the investigation, analysis, and interpretation of biomacromolecular structures. PDBe-KB brings together data from all PDB entries and displays this data as aggregated information for individual proteins, including ligand binding sites, macromolecular interactions and more. Furthermore, this community-led resource brings together structural and functional information from a host of other related resources. In this workshop, you will learn how to use the PDBe-KB aggregated views for proteins to investigate structural and function information for proteins and their associated ligands. We will also demonstrate effective use of novel visualisation components of large-scale structural data on these pages, including 3D visualisation of superposed protein structures with their bound ligands.

2.00 PDBe-KB talk (30 min) - David Armstrong
2.30 Intro to tutorials (15 min) - David Armstrong
2.45 Break (10 min)
2.55 Intro to Biochemgraph project & ligand pages (25 min) - Preeti Choudhary
3.20 PDBe-KB ligand page design session (20 min) - Preeti Choudhary
3.40 Q&A (20 min) - David Armstrong and Preeti Choudhary
4.00 End of session

Still time to register https://www.eventbrite.com/e/open-source-tools-for-chemistry-tickets-294585512197?.

 

Registration for the next batch of Open-Source Tools workshops run by the RSC Chemical Information and Computer Applications Group is now open.

https://www.eventbrite.com/e/open-source-tools-for-chemistry-tickets-294585512197?.

These workshops have been enormously popular and the interactions with the instructors have been especially valuable. Details of the next 3 workshops are described below.

All meetings start at 2 pm UK time (5 min break after 1 hour). All run using Zoom Webinar

21 April 2022 PDBe Knowledge Base (David Armstrong)

This workshop explores the Protein Data Bank in Europe Knowledge Base (PDBe-KB https://www.ebi.ac.uk/pdbe/) resource and its tools for the investigation, analysis, and interpretation of biomacromolecular structures. PDBe-KB brings together data from all PDB entries and displays this data as aggregated information for individual proteins, including ligand binding sites, macromolecular interactions and more. Furthermore, this community-led resource brings together structural and functional information from a host of other related resources. In this workshop, you will learn how to use the PDBe-KB aggregated views for proteins to investigate structural and function information for proteins and their associated ligands. We will also demonstrate effective use of novel visualisation components of large-scale structural data on these pages, including 3D visualisation of superposed protein structures with their bound ligands.

19 May 2022 KILFS database (Albert Jelke Kooistra, Andrea Volkamer )

Over the past three decades, six thousand structures of the catalytic kinase domain have been made publicly available via the Protein Data Bank. But to what extent are we making use of this wealth of information? In order to harness this data in a better way and to make it readily available for all to use in their research, KLIFS (https://klifs.net) was constructed. KLIFS, i.e. the Kinase–Ligand Interaction Fingerprints and Structures database, is a structural kinase database that systematically collects and processes all structures of the catalytic kinase domain. With the database, you can - for example - easily get a complete overview of all structures, search for ligands with a specific binding mode, identify analogs or your ligands of interest, collect data for your data mining and machine learning applications.

For this workshop, the developers of KLIFS have teamed up with the Volkamer Lab and therefore the workshop will be divided into two segments. First, Albert J. Kooistra will give an introduction to KLIFS and demonstrate different functionalities of the KLIFS website and the integration of KLIFS in KNIME via the 3D-e-Chem nodes. In the second half, Andrea Volkamer and Dominique Sydow will demonstrate, based on their new kinase-focused TeachOpenCADD workflow, how to assess kinase similarity from different data perspectives. They will emphasize their Python package KiSSim – a KLIFS-based kinase structural similarity fingerprint, and OpenCADD-KLIFS – a Python module to facilitate the integration of KLIFS data into kinase research workflows.

23 June 2022 Scoring of shape and ESP similarity (Ester Heid)

Electrostatic effects along with volume restrictions play a major role in enzyme and receptor recognition. Evaluating electrostatic and shape similarities of pairs of molecules such as proposed versus known ligands can therefore be valuable indicators of prospective binding affinities. This workshop will demonstrate how to compute electrostatic and shape similarities using the open-source tool ESP-Sim (github.com/hesther/espsim, doi.org/10.26434/chemrxiv-2021-sqvv9-v3). Available options for comparing electrostatics will be discussed interactively on selected examples of public datasets, along with advice on embedding and aligning molecules prior to computing similarities.

 

The 5th Artificial Intelligence in Chemistry is now open for both oral and poster abstract submission. This meeting will held at Churchill College 1-2 September 2022. #AIChem22

Confirmed Speakers Include

Charlotte Deane, Connor Coley, Kim Jelfs, Val Gillet, Adrian Roitberg,

You can submit your abstracts here https://hg3.co.uk/ai/.

The circular for the meeting is here https://www.rscbmcs.org/wp-content/uploads/2022/01/FINALAIinChemistry1st_Announcement.pdf

 

In 2020 RSC CICAG ran a 5 day virtual meeting on Open Source Chemical Sciences, this event had three streams Open Data. Open Publishing and Open Source tools for Chemistry. The Open Source tools for Chemistry workshops proved to be enormously popular and so CICAG held a series of monthly workshops through 2021. These workshops covered a variety of Open Source tools and resources ranging from visualisation tools, data analysis using cheminformatics toolkits, and online resources like the PDB.

These workshops were all recorded and are available on the CICAG YouTube channel, as we plan for this years workshops I thought it might be timely to remind everyone what is now available and also to thank all the presenters and developers who made the workshops possible. I've included links to all the workshops below

PDB workshop 2 using Mol*
PDB workshop 1 Registration system
Clustering using KNIME
Web apps for fragment-based drug discovery
Introduction to Cheminformatics and Machine Learning
Oxford Protein Informatics Group antibody modelling tools
Advanced DataWarrior
GNINA
Chemical Structure validation/standardisation
ChimeraX
DataWarrior
ChEMBL
UsingGoogleCoLab workshop
Fragalysis workshop
Knime workshop
PyMOL workshop

These workshops have now been viewed nearly 13,500 times and some of the comments are worth highlighting

I am not sure why this software is not famous. This is presumably the best chemoinformatics software I have seen, Great presentation!

Two hours of distilled pure science.

These workshops were sponsored by Liverpool Chirochem.

 

For any scientists working with biomolecules be it, medicinal chemist, structural biologist, biochemist etc. the most valuable source of primary structural information is the Protein Data Bank (PDB). This resource has now been running for 50 years so it very timely to hear about the history of the RCSB PDB and the different components that make up the repository both from a depositor and a user. The second workshop describes some of the recent changes in particular the development of Mol* a 3D viewer capable of rendering from macromolecular assemblies down to atomic details.

Workshop 1

• History of the Protein Data Bank (PDB) and the Worldwide PDB Stephen K. Burley, RCSB Protein Data Bank
  
• PDBx/mmCIF Data Standard and PDB Data Deposition with OneDep Ezra Peisach and Jasmine Young
  
• Small Molecules in the PDB -talk + tutorial Chenghua Shao, RCSB Protein Data Bank
  
• OneDep Tutorial - Jasmine Young and Ezra Peisach
  

Workshop 2

• wwPDB Validation: Assessing the Quality of PDB structures John Berrisford, Protein Data Bank in Europe
• How to Interpret the Quality of a PDB Structure using the wwPDB validation report - tutorial David Armstrong/John Berrisford/Jack Turner, Protein Data Bank in Europe
• 3D Visualisation of PDB Data with the Mol* viewer -James Tolchard, Protein Data Bank in Europe
• Impact of AI and Future of PDB Data: Next Generation PDB Archive - Sameer Velankar, Protein Data Bank in Europe
• Round Table Discussion - Sameer Velankar, Protein Data Bank in Europe, Stephen K. Burley, RCSB Protein Data Bank

Workshop 1

Workshop 2

This is part of the RSC CICAG workshops on Open Chemical Sciences, all 17 workshops are on the RSC CICAG YouTube playlist https://www.youtube.com/playlist?list=PLBQwbn0mPhvWfOx6ce_vUjr54ftLBmSH0.

If you have any suggestions (or would like to volunteer) for future workshops feel free to get in touch.

 

Registration for the November RSC CICAG workshops is open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

Given that it is the 50th anniversary of the PDB archive it is appropriate that the two final workshops for 2021 are describing this absolutely invaluable resource.

Protein Data Bank Workshop (16 November 2021 15.00 – 17.00 GMT)

The Protein Data Bank https://www.wwpdb.org archives information about the 3D shapes of proteins, nucleic acids, and complex assemblies that help students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. Open access PDB data are used by hundreds of data resources and millions of users exploring fundamental biology, energy, and biomedicine. The PDB is a vast resource and this workshop will be invaluable to anyone seeking to get full value from the PDB.

Mol* Workshop (18 November 2021 15.00 – 17.00 GMT)

Mol* is a modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data. More information can be found here: https://molstar.org. High-performance graphics and data handling of the Mol* Viewer allow users to simultaneously visualise up to hundreds of (superimposed) protein structures, play molecular dynamics trajectories, render cell-level models at atomic detail with tens of millions of atoms, or display huge models obtained by I/HM such as the Nuclear Pore Complex.

David Sehnal, Sebastian Bittrich, Mandar Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K Burley, Jaroslav Koča, Alexander S Rose: Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures, Nucleic Acids Research, 2021; DOI.

If you want to learn more about the history of the PDB there is a video here.

These workshops are sponsored by Liverpool ChiroChem

 

The latest RSC CICAG Open-Source Tools for Chemistry Workshop is now on YouTube. RSC CICAG Open Source Tools for Chemistry :- Clustering using KNIME.

Clustering is an invaluable cheminformatics technique for subdividing a typically large compound collection into small groups of similar compounds. One of the advantages is that once clustered you can store the cluster identifiers and then refer to them later, this is particularly valuable when dealing with very large datasets. Clustering is often used in the analysis of high-throughput screening results, or the analysis of virtual screening or docking studies.

There is a comparison of clustering options here.

The previous 14 workshops are available on a CICAG YouTube playlist.

You can still register for next months workshops here https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617.

 

Just got this message from Greg Landrum

The workshop tomorrow will have a hands-on component. This isn't mandatory, but I think you'll get more from the workshop if you follow along with what we're doing in your own local copy of the workflow.

In order to get you started and make sure that you have all the KNIME pieces that you need installed, I created a space in the public KNIME hub for the workshop and have uploaded some introductory material there:

https://hub.knime.com/greglandrum/spaces/Public/latest/Presentations/2021/20211020RSCWorkshop/ClusteringIntro.

If you are logged into the KNIME hub (registration is free), you can download the workflow and data by simply using the download button:

Once you've downloaded the workflow package, you should be able to import everything into the KNIME Analytics Platform by double clicking the "ClusteringIntro.knar" file which is downloaded.

If for some reason you don't want to register, then you'll need to navigate to the page for the workflow and the Data folder, download everything individually, and import them into KNIME Analytics Platform manually. You should be able to find information online for how to do this, but I won't be able to help you with this during the workshop due to time constraints.

When you open the 01_Clustering workflow, you may be asked if you want to install missing extensions. Please do this in order to ensure that you have everything necessary to follow along during the workshop. Everything we install as part of this process is free and open source.

Shortly before the workshop starts I will share an additional workflow which we'll use for the main part of the workshop. I'll give you this link during the workshop.

Note that the sample workflows we are using were created with KNIME 4.4 (the version released this summer). For workshops like this we like to use recent versions of KNIME so that we can show you the newest features and capabilities. If you have an older version of KNIME things may or may not work correctly and you may have to replace one or more of the nodes with older equivalents.

You can download KNIME here https://www.knime.com/downloads

The next RSC CICAG Open Source Tools for Chemists workshop will be held next week.

23 September 2021 14.00 – 16.00 GMT

Web apps for fragment-based drug discovery, fragalysis and more with Rachael Skyner, Diamond Light Source More information about fragalysis at Diamond can be found here: https://fragalysis.diamond.ac.uk/viewer/react/landing.

Registration for these free workshops is now open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

These workshops are sponsored by Liverpool ChiroChem

 

The RSC Chemical Information and Computer Applications Group (CICAG) workshop YouTube videos https://www.youtube.com/c/RSCCICAG have now been watched nearly 8000 times. A number of folks have asked about future workshops and CICAG activities.

The details of the future workshops are here on Eventbrite all workshops are free to attend. We will be thinking about possible workshops for 2022 soon, so feel free to suggest ideas.

CICAG are also co-organisers of the 4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Monday-Tuesday, 27th-28th September 2021 full details are here.

If you want to keep in touch with CICAG activities there are several options. If you are an RSC member then you can choose to join the interest group.

When you renew your Royal Society of Chemistry membership you can choose “Chemical Information and Computer Applications Group” (group 86) as one of your groups to be a member of. If you have already submitted your form you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141).

If you are not an RSC member you can follow CICAG activities on Twitter or on LinkedIn

The video of the latest RSC CICAG Open Source Tools for Chemistry is now online.

Part of the RSC CICAG Open Chemical Sciences workshop series. Workshop given by Pat Walters (http://practicalcheminformatics.blogspot.com) entitled "An introduction to cheminformatics, data analysis and machine learning".

A hands-on workshop on building and validating ML models, including:

• Initial exploratory data analysis
• ML model building
• Model evaluation
• Making predictions on a larger data set

The notebooks for the tutorial are here https://mybinder.org/v2/gh/PatWalters/chem_tutorial/HEAD. If there are any problems, you should be able to just reload the page. The code and notebooks are in a GitHub repo.

The video is here YouTube.

More workshop videos are available on the RSC CICAG playlist

 

An updated program for the 4th RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Meeting is now available and there is the usual excellent range of speakers. Registration is now open https://www.maggichurchouseevents.co.uk/bmcs/AI-2021onlineregistration.htm. There are also opportunities for sponsorship.

Confirmed Speakers

Keynote: AI for molecular design, past, present and future Ola Engkvist, AstraZeneca, SE

Keynote: Challenges and opportunities for machine learning in drug discovery Patrick Walters, Relay Therapeutics, US

PyPEF – an integrated framework for data-driven protein design and engineering Mehdi Davari, Leibniz Institute of Plant Biochemistry (IPB), DE

Efficient ML strategies to explore chemical reactivity Fernanda Duarte, University of Oxford, UK

Exploring molecular space and accelerating drug discovery with MegaMolBART, a transformer-based generative model Michelle Gill, NVIDIA, US

Machine learning models for predicting human in vivo PK parameters using chemical structure and dose Olga Obrezanova, AstraZeneca, UK

Molecular transformer-aided biocatalysed synthesis planning Daniel Probst, IBM Research Europe, CH

Best practice for chemical language model de novo design of GPCR ligands: datasets, scoring functions and optimization algorithms Morgan Thomas, University of Cambridge, UK

Presentation title to be confirmed (provisional) Andrea Volkamer, Charité Universitätsmedizin Berlin, DE

‘Attending’ to co-crystals in the Cambridge Structural Datacenter Aikaterini Vriza, University of Liverpool, UK

Driving lead optimisation with BRADSHAW Ian Wall, GlaxoSmithKline, UK

 

The next of the monthly RSC CICAG workshops is on 19 August 2021 is entitled "An introduction to cheminformatics, data analysis and machine learning" with Pat Walters, Relay Therapeutics and blogger, if you don't follow his blog have a look now http://practicalcheminformatics.blogspot.com.

This will be a hands-on workshop on building and validating ML models, including:

• Initial exploratory data analysis
• ML model building
• Model evaluation
• Making predictions on a larger data set

I'm sure this will be a really invaluable experience. Over 150 have already registered and you can register using the link below.

Registration for these free workshops is now open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

These workshops are sponsored by Liverpool ChiroChem

 

Part of the RSC Open Chemical Sciences workshop series. Workshop given by Charlotte Deane, Fergus Boyles and Matthew Raybould on the OPIG (Oxford Protein Informatics Group) antibody modelling tools. https://www.blopig.com/blog/2020/09/what-can-you-do-with-the-opig-antibody-suite-v2-0/ The OPIG Antibody Suite? V2.0 is a collection of informatics tools and databases, including CoV-AbDab: the coronavirus antibody database https://academic.oup.com/bioinformatics/article/37/5/734/5893556. Now available on YouTube

Download for workshop materials http://macinchem.org/Temp/OPIGworkshop.zip.

Registration for future free workshops is open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21) Liverpool Chirochem sponsor the Open-Source Tools for Chemistry Workshop series.

 

The next of the monthly RSC CICAG workshops sponsored by Liverpool ChiroChem is on June 24 featuring DataWarrior, and over 250 have registered. These workshops are usually in the third week of each month on Thursday (or within a day or two) you can find out more about the future workshops in the series and register using the link below.

Registration for these free workshops is now open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

The RSC CICAG Open Source tools workshop on DataWarrior is on 24 June

Registration is free and you will be sent login details at a later date. Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

DataWarrior combines dynamic graphical views and interactive row filtering with chemical intelligence. Scatter plots, box plots, bar charts and pie charts not only visualize numerical or category data, but also show trends of multiple scaffolds or compound substitution patterns. Chemical descriptors encode various aspects of chemical structures, e.g. the chemical graph, chemical functionality from a synthetic chemist’s point of view or 3-dimensional pharmacophore features.

If you have any questions about how to do things in DataWarrior please feel free to send them in.

All scientists working Chemistry need software tools for accessing, handling and storing chemical information, or performing molecular modelling and computational chemistry. There is now a wealth of open-source tools to help in these activities, however many are not as well-known as commercial offerings.

These workshops offer a unique opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry.

 

The latest in the Open Source tools for Chemistry, fantastic workshop using GNINA for docking.

GNINA 1.0 by David Koes. The use of docking to predict ligand binding to a receptor is now well established, this workshop will cover docking and structure-based virtual screening, with an introduction to the theory followed by practical examples. The slides for the Molecular Docking with GNINA 1.0 workshop are here and the Jupyter Notebooks are here.

 

All scientists working Chemistry need software tools for accessing, handling and storing chemical information, or performing molecular modelling and computational chemistry. There is now a wealth of open-source tools to help in these activities, however many are not as well-known as commercial offerings.

These workshops offer a unique opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry.

Our aim is to have a once a month workshop, usually the third week of each month on Thursday (or within a day or two).

Registration for these free workshops is now open https://www.eventbrite.com/e/open-source-tools-for-chemistry-workshops-tickets-156431429617. (#OpenChem21)

22nd July 2-4 pm (UK time) Charlotte Deane workshop on the OPIG (Oxford Protein Informatics Group) antibody modelling tools. https://www.blopig.com/blog/2020/09/what-can-you-do-with-the-opig-antibody-suite-v2-0/ The OPIG Antibody Suite? V2.0 is a collection of informatics tools and databases, including CoV-AbDab: the coronavirus antibody database https://academic.oup.com/bioinformatics/article/37/5/734/5893556.

19th August 2-4 m (UK time) Pat Walters Relay Pharm and http://practicalcheminformatics.blogspot.com an introduction to Cheminformatics, data analysis and machine learning. A hands-on workshop on building and validating ML models.
- Initial exploratory data analysis - ML model building - Model evaluation - Making predictions on a larger dataset

23rd September 2-4 pm (UK time) Rachel Skyner https://fragalysis.diamond.ac.uk/viewer/react/landing and https://twitter.com/rachaelskyner Web apps for fragment based drug discovery, fragalysis and more.

21st October 2-4 pm (UK time) Daria Goldmann https://www.knime.com KNIME workshop. KNIME Analytics Platform is the open source software for creating data science. Intuitive, open, and continuously integrating new developments, KNIME makes understanding data and designing data science workflows and reusable components accessible to everyone. Knime can be downloaded here https://www.knime.com/downloads .

16th November 3-5 pm (UK time) PDB https://www.wwpdb.org workshop to coincide with PDB 50th anniversary. The Protein Data Bank archives information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

18th November 3-5 pm (UK time) Mol* https://molstar.org workshop, Mol* is a modern web-based open-source toolkit for visualisation and analysis of large-scale molecular data.

 

The videos for the first two workshops sponsored by LiverpoolChiroChem are now on the CICAG YouTube channel.

21 April Chemical Structure validation/standardisation (Greg Landrum) Possibly the most important step in model or database building is data curation, this workshop will deal with chemical structure validation and standardisation. https://youtu.be/eWTApNX8dJQ.

25th March ChimeraX (https://www.rbvi.ucsf.edu/chimerax/) (Tom Goddard) Intro to ChimeraX for visualizing proteins, ligands and X-ray and electron microscopy maps. https://youtu.be/M2K72Kgk718.

The next workshops are

• 27 May GNINA 1.0 (https://chemrxiv.org/articles/preprint/GNINA10MolecularDockingwithDeep_Learning/13578140) (David Koes) The use of docking to predict ligand binding to a receptor is now well established, this workshop will cover docking and structure-based virtual screening, with an introduction to the theory followed by practical examples.

• 24 June Advanced DataWarrior (http://www.openmolecules.org/datawarrior/) Isabelle Giraud. The previous very popular introductory workshop brought DataWarrior to a new, wider audience, this workshop will highlight advanced features, macros and other topics that were brought up by users. So feel free to submit requests.

Registration is free and you will be sent login details at a later date.

Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

 

The AI 4 Proteins Seminar Series 2021 is now in full swing, the first two presentations by Lucy Colwell and Melanie Vollmar were really brilliant and are now on the CICAG YouTube channel https://www.youtube.com/c/RSCCICAG.

You can find out more about the forthcoming events in the series here https://www.ai3sd.org/ai3sd-online-seminar-series/ai4proteins-seminar-series-2021/.

The final event is 2 day meeting on Protein Structure Prediction. This looks like it will be a great meeting with a fantastic lineup. Current invited speakers include: Professor Debora Marks (Harvard University), Professor Cecilia Clementi (Freie Universität Berlin), Professor Charlotte Deane (University of Oxford), Professor Tudor Oprea (University of New Mexico), Dr Derek Lowe (Novartis) and Professor Stephen Burley (RCSB PDB, Rutgers University, USCD).

There is still time to submit abstracts for short talks and posters.

Short Talk Abstract Submission Form. Deadline: 29/04/2021. Notification of Acceptance: 06/05/2021.
Poster Abstract Submission Form. Deadline: 29/04/2021. Notification of Acceptance: 06/05/2021.
Poster & Video Guidelines for Accepted Posters

Full details are here https://www.ai3sd.org/ai3sd-event/17-06-2021-ai3sd-rsc-cicag-protein-structure-prediction/.

 

The next CICAG Open Source tools workshop is coming up.

21 April Chemical Structure validation/standardisation (Greg Landrum) Possibly the most important step in model or database building is data curation, this workshop will deal with chemical structure validation and standardisation.

Registration is free and you will be sent login details at a later date.

Register here https://cicag-open-source-tools-for-chemistry.eventbrite.com/.

These workshops are sponsored by LiverpoolChiroChem.

Some pre-event details for the upcoming workshop

The workshop will be hands-on, so you'll get the most out of it if you have the most recent versions of the RDKit and the ChEMBL Structure Pipeline installed. You can download a conda environment specification here that will create a minimal environment which should have everything you need for the workshop. The conda environment uses python 3.7 since that's what's available on google colab, but you should also be able to use python 3.8 or 3.9 without problems; just change the python version spec in the environment file.

I'll be using a sample dataset from PubChem Substance: https://ftp.ncbi.nlm.nih.gov/pubchem/Substance/CURRENT-Full/SDF/Substance000000001000500000.sdf.gz

If you have problems creating (or don't want to create) a local environment, I also created a notebook  in google colab which you can use. The cells at the beginning of this notebook install all required software and download the sample dataset: https://colab.research.google.com/drive/1p33LA610-8SS4p5-F1DrAlmB31T8F-KB?usp=sharing
Best, -greg

 

The Emerging Technologies Competition is the Royal Society of Chemistry’s annual initiative for early stage companies and academic entrepreneurs who want to commercialise their technologies to make a societal impact.

The competition is a European programme seeking to identify start-ups and spin outs who are developing the most novel, innovative and promising chemistry tech.

More details here https://www.rsc.org/competitions/emerging-technologies/

Closing date for applications April 18th.

Winners will.....

• Receive a cash prize of £20,000 (per competition category)
• Be assigned a Royal Society of Chemistry mentor who will provide ongoing support for one year
• Through discussion with their mentor, winners, who are an incorporated company, can be provided a business acceleration grant up to the value of £20,000
• Gain wider support and advice from our competition partners and judges, during the final

 

The video of the ChimeraX workshop is now online https://youtu.be/M2K72Kgk718.

The RSC CICAG YouTube channel is building up a very useful collection of videos https://www.youtube.com/c/RSCCICAG.

 

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

 

Around this time last year RSC CICAG held a meeting to discuss 20 years of rule of 5 this meeting involved presentations but also less formal panel discussions and informal chats. This proved to be really popular and CICAG had planned to hold another end of year meeting again with the aim of fostering more informal interactions. However, the efforts involved in converting the AI in chemistry and the Open Chemical Science meetings from physical to virtual meetings meant that we had to postpone the end of year meeting till next year.

In its place we have organised an impromptu webinar looking back at the history of subjects at the core of CICAG's interests.

Andrew Dalke has kindly agreed to talk about the history of cheminformatics from punch cards to the present day.

John Overington will also talk about the history of ChEMBL an absolutely invaluable open-source database that we now take for granted.

Our aim is that we will try to make this informal with plenty of time to ask questions/reminisce so stock up on mince pies and mulled wine, click the link below and settle back for a fascinating hour or two.

You are invited to a Zoom webinar.

When: Dec 22, 2020 04:00 PM London Topic: Looking back at Cheminformatics and ChEMBL

Register in advance for this webinar: https://us02web.zoom.us/webinar/register/WN_-bWCQe32RW6ZKVEyb8qq4A

After registering, you will receive a confirmation email containing information about joining the webinar.

I promised a recipe.

Mulled Wine

Whilst you can buy bottles of mulled wine I think making your own gives better results (we are chemists after all).

Ingredients

A bottle of inexpensive red wine
2 oranges
2 cinnamon sticks
4 Cloves
2 Star anise
30 g Sugar (or more to taste)

Pour the red wine into a saucepan and add the cinnamon sticks (you can use ground cinnamon), cloves and star anise. Then add the zest from one of the oranges plus the orange juice together with the sugar. Heat gently to dissolve sugar and the simmer on low heat for 10 mins.

Serve whilst warm and add orange slices to decorate.

You can add a little brandy or Grand Marnier to give a little extra kick.

 

Just a couple of notes for software installs prior to the event for those attending the free online Workshop on Open-Source Tools for Chemistry 9-13 November 2020.

Monday 13-30 to 15-30 Cheminformatics and Data Analysis using DataWarrior (Isabelle Giraud)

DataWarrior can be downloaded from here http://www.openmolecules.org/datawarrior/download.html

The training files can all be downloaded from here

Monday 16 - 00 to 18-00 Molecular visualisation using Pymol (Garrett Morris)

Software to install:

PyMOL via Conda:
Conda: https://www.anaconda.com/distribution/ or Miniconda: https://docs.conda.io/en/latest/miniconda.html
https://anaconda.org/psi4/pymol or https://omicx.cc/2019/05/26/install-pymol-windows/

PyMOL via MacPorts:
http://www.ub.edu/cbdd/?q=content/installing-pymol-macports
% sudo port install tcl -corefoundation
% sudo port install tk -quartz
% sudo port install pymol

PyMOL from GitHub: https://github.com/schrodinger/pymol-open-source

Tuesday 11 to 13-00 Chemistry in the cloud: leveraging Google Colab for quantum chemistry (Jan Jensen)

Participants should download Chrome and have a Google account
Participants should make sure they can access this page: https://bit.ly/37fIYbp.
Some basic degree of Python proficiency is required for the course

It would be great if participants could fill out this survey https://forms.gle/pjwsnJTb4X6QpiHK9 early enough to help me design the course

Wednesday 13-30 to 15-30 Accessing biological and chemical data in ChEMBL (Anna Gaulton)

Requires a modern web-browser (with javascript not blocked) such as Chrome/Safari

Thursday 16-00 to 18-00 Fragment based screening, XChem at Diamond (Rachel Skyner)

Requires Chrome web browser, if there is time Rachel would like to give an introduction to the new Python API, we can go through the installation at the workshop but you must have Anaconda installed.

Friday 11-00 to 13-00 An introduction to KNIME workflows (Greg Landrum)

Knime can be downloaded here https://www.knime.com/downloads

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

More details and registration can be found here https://www.rsc.org/events/detail/43180/workshop-on-open-source-tools-for-chemistry.

Last Updated 28 October 2020

 

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.

 

All scientists working in chemistry need software tools for accessing, handling and storing chemical information, or performing molecular modelling and computational chemistry. There is now a wealth of open-source tools to help in these activities; however, many are not as well-known as commercial offerings. This workshop offers a unique opportunity for attendees to try out a range of open-source software packages for themselves with expert tuition in different aspects of chemistry.

The software packages will be presented over six two-hour sessions as follows:

09 November: 13.30 - 15.30 Cheminformatics and data analysis using Data Warrior (Isabelle Giraud) 09 November: 16.00 - 18.00 Molecular visualization using PyMOL (Garrett M Morris)

10 November: 11.00 - 13.00  Chemistry in the cloud: leveraging Google Colab for quantum chemistry  (Jan Jensen)

11 November: 13.30 - 15.30  Accessing biological and chemical data in ChEMBL (Anna Gaulton)

12 November: 16.00 - 18.00  Fragment-based screening, XChem at Diamond (Rachael Skyner)

13 November: 11.00 - 13.00  Interactive and automated chemical data analysis with KNIME (Greg Landrum)

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

More details and registration can be found here https://www.rsc.org/events/detail/43180/workshop-on-open-source-tools-for-chemistry.

 

The heavily oversubscribed 3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry will taking place 28th-29th September 2020 Twitter hashtag - #AIChem20. This has been converted to a virtual event and those registered will be getting more details soon.

There is an accompanying poster session, the posters are being hosted on twitter and you can see them all using the hashtag AIChem20posters. A number of the poster presenters have also created 2 min lightning presentations which will be uploaded to YouTube once the last few presentations have been included.

If you are registered and find you can no longer attend, please send an e-mail to the BMCS Secretariat promptly, so that your place can be allocated to one of those on the waiting list.

 

Registration is open!!

• Event 3rd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry
• Dates Monday-Tuesday, 28th-29th September 2020
• Format A virtual event
• Organisers RSC BMCS and RSC CICAG (Royal Society of Chemistry’s Biological and Medicinal Chemistry Sector, and Chemical Information and Computer Applications Group)
• Websites https://www.maggichurchouseevents.co.uk/bmcs. Also https://www.rsc.org/events/detail/42785/3rd-rsc-bmcs-rsc-cicag-artificial-intelligence-in-chemistry
• Twitter #AIChem20

Synopsis.
Artificial Intelligence is presently experiencing a renaissance in development of new methods and practical applications to ongoing challenges in Chemistry. Following the successes of two “Artificial Intelligence in Chemistry” meetings in 2018 and 2019, we are pleased to announce that the Biological & Medicinal Chemistry Sector (BMCS) and Chemical Information & Computer Applications Group (CICAG) of the Royal Society of Chemistry are once again organising a conference to present the current efforts in applying these new methods. The meeting will be held over two days and combine aspects of artificial intelligence and deep machine learning methods to applications in chemistry

The Call for Abstracts is Open.
Applications for both oral and poster presentations are invited. Posters will be displayed during a dedicated poster session and, at the time of submission, applicants are asked if they wish to provide a two-minute lightning oral presentation. The closing date for all submissions is Friday, 31st July.

There will be a mix of plenary and keynote talks as well as poster sessions with some lightning poster talks. There will also be exhibitor sessions, and we are currently exploring options for providing breakout rooms for discussions.

Confirmed Speakers
Teaching neural network to attach and detach electrons from molecules
Keynote: Olexandr Isayev, Carnegie Mellon, US

DNA-encoded small molecules libraries meet machine learning
Keynote: Patrick Riley, Google, US

Artificial neural network enhanced synthesis and retrosynthesis prediction
Esben Jannik Bjerrum, AstraZeneca, SE

Machine learning for free energy calculations
Hannah Bruce McDonald, Memorial Sloan Kettering Cancer Center, US

Data driven representations for predicting molecular properties: benchmarking and applications in generative chemistry
Jessica Lanini, Novartis, CH

Using machine learning for molecular dynamics simulations
Sereina Riniker, ETH Zürich, CH

Registration Participation is free of charge, although registration is required so we can ensure the numbers are covered by the virtual meeting software license:
- online via this link (no payment required) I

AI - second announcement

 

The latest RSC Chemical Information and Computer Applications Group newsletter is out.

https://www.rsc.org/images/CICAGNewsletterSummer2020tcm18-252147.pdf

• Chemical Information & Computer Applications Group Chair's Report
• CICAG Planned and Proposed Future Meetings
• Open Chemical Science Online Webinars & Workshops in 2020
• Time to add "Cheminformatics" to Keywords Indexing Science
• COVID-19 and the Identification of "Drug Candidates"
• DP4-AI: High-Throughput Automatic Assignment of NMR Spectra
• The Collaborative Computational Project Number 4 Release 7.1
• Meeting Report: AI & ML in Drug Discovery Meeting
• Predicting the Activity of Drug Candidates when there is no Target
• News from CAS
• News from AI3SD
• Other Chemical Information Related News

Huge thanks to all who contributed.

 

The RSC Chemical Information and Computer Applications Group in collaboration with the SCI Fine Chemicals Group have just finished a series of virtual workshops on Computational Tools for Drug Discovery. This series of events was put together to replace a physical one-day workshop due to be held in Leeds. The one day event would have been able to accommodate 50-60 attendees and I'm delighted to report that the online Wednesday workshops were attended by a total of 538 people, so we were able to support an order of magnitude larger audience.

I'd like to thank all the companies that participated in the workshops,

• MedChemica - MedChemica’s MCPairs Online - An idea generation tool based on Matched Molecular Pair Analysis and Machine Learning.
• OpenEye - Practical drug discovery in the cloud using ORION.
• Cresset - Combining ligand and structure-based approaches to improve molecule design using Cresset desktop solutions.
• CCDC - Structure-based drug design with CSD-Discovery.
• Optibrium - Guided Multi-Parameter Optimisation of 2D and 3D SAR.
• KNIME - An interactive workflow for hit list triaging.
• CDD Vault – Managing, Archiving, Mining, Reporting, and Analyzing Collaborative Drug Discovery Data

The feedback from attendees has been very positive and there will now be a short break whilst we organise the next series of workshops for later in the year.

 

The election of the new president of the RSC is upon us, there are a number of excellent candidates but I'd like to draw attention to one.

I've known David Rees for many years and I can't think of a better person to lead the RSC at the present time. A really top class scientist with an excellent career in Drug Discovery, whilst maintaining contacts with academic research and holding important roles within the RSC.

If one thing COVID-19 has taught is we need to increase support for collaboration between Academia and Industry in healthcare, but also we should not lose sight of the oncoming challenges set by climate change. These are major challenges and we need build further collaborations.

Diversity is correctly high on many peoples radar, but David is someone who realises diversity goes beyond gender and is a great supporter of providing opportunities to all.

For a while I think chemistry has been thought of as simply a service, recent events have underlined chemistry as a key component of research and the economy, we need to take the opportunity for the RSC to take a leading role in ensuring that the recent momentum is maintained, and David would be a passionate advocate.

All RSC members should have received a unique voter code, and I hope you all take the opportunity to vote.

This year, the RSC are holding elections for the following positions:

• RSC President (one vacancy)
• Elected member of Member Communities Board (two vacancies - one representative of Interest Groups; one representative of Local Sections)
• Elected member of Professional Standards Board (one vacancy)
• Elected member of Analytical Division Council (two vacancies)
• Elected member of Chemistry Biology Interface Division Council (two vacancies)
• Elected member of Dalton Division Council (two vacancies)
• Elected member of Education Division Council (two vacancies)
• Elected member of Environment, Sustainability and Energy Division Council (two vacancies)
• Elected member of Materials Chemistry Division Council (two vacancies)

 

The latest issue of the RSC CICAG newsletter is now available online, the winter 2019 issue has continued the trend to include more original content and news on chemical information.

This issue includes

• Chemical Information & Computer Applications Group Chair's Report
• CICAG Planned and Proposed Future Meetings
• Periodic Table brought to life at Catalyst!
• From Nantwich to Oxygen: Joseph Priestley’s Journey of Discovery
• Dr Andy Vinter 1943 - 2019
• Open Force Field Initiative on Energetics for Molecular Modelling
• Obituary Dr William Geoffrey Town
• Extending InChI to Include Inorganic & Organometallic Compounds
• Wendy Warr named 2020 Herman Skolnik Award Winner
• A Practical Case for WebAssembly
• Tony Kent Strix Award and Annual Lecture 2019
• Meeting Report: 20 Years of the Rule of Five
• Meeting Report: 2nd RSC BMCS & CICAG AI in Chemistry Meeting
• Chemical Information / Cheminformatics and Related Books
• News from CAS
• News from the RSC
• News from AI3SD

This newsletter also includes articles from Prof David Mobley, Dr Wendy Warr, Dr Alex M Clark, Jane List, Dr Rajarshi Guha and Dr Dan Ormsby, and CICAG is very appreciative of these external contributions to this widely-read publication. If readers have any suggestions for contributions that would be of interest to the CICAG community, please get in touch.

Past issues of the newsletter are available on the website.

 

My Royal Society of Chemistry annual subscription letter just arrived. This is a good time to think about Interest Group membership, if you are a member of the RSC you can join several interest groups for free, however disappointingly many people fail to take advantage of this opportunity.

Interest Groups are scientific networks run by members for their community. Each group is themed around a specific area or application of the chemical sciences. They organise an annual series of events to cater for both their members and the wider scientific community. These events vary from: multi-day conferences and workshops to training events.

The Chemical Information and Computer Applications Group (CICAG) is one such group (Group number 86), you can find out more on the CICAG website.

The storage, retrieval, analysis and preservation of chemical information and data are of critical importance for research, development and education in the chemical sciences. All chemists, and everybody else who works with chemical substances, need tools and techniques for handling chemical information.

CICAG works to:

• Support users of chemical information, data and computer applications and advance excellence in the chemical sciences
• Inform RSC members and others of the latest developments in these rapidly evolving areas;
• Promote the wider recognition of excellence in chemical information and computer applications at this level

This year CICAG has been involved in a workshop on Computational Tool for Drug Discovery, 2nd Conference on Artificial Intelligence in Chemistry, and the 20 Years of Rule of Five Meeting. In addition CICAG has supported the Sheffield Cheminformatics Meeting, Dial a Molecule, Artificial Intelligence and Augmented Intelligence for Automated Investigations for Scientific Discovery network and the In Silico Toxicology Networking Meeting. In addition to other outreach activities.

RSC CICAG publish a regular Newsletter which keeps members in touch with the Group's activities and includes articles, reviews of interest, news and events.

If you would like to join the group you can do so by adding interest group 86 to the last page of the renewal form and returning it to the RSC or you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141).

 

The 2nd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry is now over, two intensive days of presentations and posters. Many thanks for all who took part and made it such a successful event.

Special mention to the Poster prize winners.

P17 by Jenke Scheen of the University of Edinburgh Entitled: "Improving the accuracy of alchemical free energy methods by learning correction terms for binding energy estimates"

P6 by Adam Green of the University of Leeds Entitled: "Activity-directed discovery of inhibitors of the p53/MDM2 interaction: towards autonomous functional molecule discovery"

P3 by Ya Chen of the University of Hamburg Entitled: "NP-Scout: machine learning approach for the identification of natural products and natural product-like compounds in large molecular databases"

If you want to browse through the Twitter feeds search for the #AIChem19 hashtag.

Many of the presentations are now available in pdf format on the meeting website.

We are already thinking about a possible 3rd meeting, and any feedback would be much appreciated.

 

I was just looking through the delegate registrations for the 2nd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Meeting taking place in Cambridge, UK 2nd to 3rd September 2019. We now have significantly more registrations than the first meeting, participants are coming from 16 different countries and whilst the UK and US predominate there are many participants from the rest of Europe and even some from Japan and Korea. There are 90 different organisations represented and I'm delighted to see there are over 20 student attendees, many from overseas. A number of students are presenting posters and the lineup of people taking part in the flash poster session can be found here.

Registration is still open for what looks like what will be another outstanding meeting.

A few people have said they are planning a visit to Cambridge for a holiday around the meeting and have asked for suggestions of things to do. Visit Cambridge is a good place to start.

 

Just finished the RSC CICAG committee meeting and one of the discussion items was support for people to attend conferences and meetings. CICAG is committed to supporting attendance at our meetings in as many ways as possible. We always ensure that the venue supports wheelchair access and that any meals accommodate any dietary requirements that have been gathered on registration.

We offer student bursaries to help cover registration, travel, and accommodation if required. These are detailed on the individual conference pages. If you are making a particularly lengthly journey and need additional help please get in touch and we will see what we can do to help.

There are also travel grants Travel grants both for students and early career scientists https://www.rsc.org/ScienceAndTechnology/Funding/division-travel-grants/index.asp to attend conferences or workshops.

A recent addition are awards for carers https://www.rsc.org/campaigning-outreach/campaigning/incldiv/grants-for-carers/ caring responsibilities are wide and varied, but they can sometimes be hard to balance alongside attending conferences.

If you have any other suggestions feel free to email cicagrsc@gmail.com

Upcoming meetings

2nd RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Website
Twenty Years of the Rule of Five Website.

 

I ran a poll last week asking "In which area is Artificial Intelligence likely to most impact Chemistry?" And we now have the results.

Whilst Molecular Design was the most popular choice it was interesting to see that all options were well supported. This suggests that there are opportunities for artificial intelligence to have an impact in many facets of chemistry. I'm delighted to see this since this was part of the thinking behind the AI in Chemistry meeting and I think the line up of speakers will have something for everyone.

2nd RSC-BMCS / RSC-CICAG, Artificial Intelligence in Chemistry, Monday-Tuesday, 2nd to 3rd September 2019. Fitzwilliam College, Cambridge, UK. #AIChem19

Synopsis
Artificial Intelligence is presently experiencing a renaissance in development of new methods and practical applications to ongoing challenges in Chemistry. Following the success of the inaugural “Artificial Intelligence in Chemistry” meeting in 2018, we are pleased to announce that the Biological & Medicinal Chemistry Sector (BMCS) and Chemical Information & Computer Applications Group (CICAG) of the Royal Society of Chemistry are once again organising a conference to present the current efforts in applying these new methods. The meeting will be held over two days and will combine aspects of artificial intelligence and deep machine learning methods to applications in chemistry.

Programme (draft)

Monday, 2nd September
08.30
Registration, refreshments
09.30
Deep learning applied to ligand-based de novo design: a real-life lead optimization case study
Quentin Perron, IKTOS, France
10.00
A. Turing test for molecular generators
Jacob Bush, GlaxoSmithKline, UK
10.30
Flash poster presentations
11.00
Refreshments, exhibition and posters
11.30
Presentation title to be confirmed
Keynote: Regina Barzilay, Massachusetts Institute of Technology, USA
12.30
Lunch, exhibition and posters
14.00
Artificial intelligence for predicting molecular Electrostatic Potentials (ESPs): a step towards developing ESP-guided knowledge-based scoring functions
Prakash Rathi, Astex Pharmaceuticals, UK
14.30
Molecular transformer for chemical reaction prediction and uncertainty estimation
Alpha Lee, University of Cambridge, UK
15.00
Drug discovery disrupted - quantum physics meets machine learning
Noor Shaker, GTN, UK
15.30
Refreshments, exhibition and posters
16.00
Application of AI in chemistry: where are we in drug design?
Christian Tyrchan, AstraZeneca, Sweden
16.30
Presentation title to be confirmed
Anthony Nicholls, OpenEye Scientific Software, USA
17.30 Close
18.45 Drinks reception
19.15 Conference dinner

Tuesday, 3rd September
08.30
Refreshments
09.00v Deep generative models for 3D compound design from fragment screens
Fergus Imrie, University of Oxford, UK
09.30
DeeplyTough: learning to structurally compare protein binding sites
Joshua Meyers, BenevolentAI, UK
10.00
Discovery of nanoporous materials for energy applications
Maciej Haranczyk, IMDEA Materials Institute, Spain
10.30
Refreshments, exhibition and posters
11.00
Deep learning for drug discovery
Keynote: David Koes, University of Pittsburgh, USA
12.00
Networking lunch, exhibition and posters
14.00
Presentation title to be confirmed
Olexandr Isayev, University of North Carolina at Chapel Hill, USA
14.30
Dreaming functional molecules with generative ML models
Christoph Kreisbeck, Kebotix, USA
15.00
Refreshments, exhibition and posters
15.30
Presentation title to be confirmed
Keynote: Adrian Roitberg, University of Florida, USA
16.30
Close

You can get more information and register here https://www.maggichurchouseevents.co.uk/bmcs/AI-2019.htm.

 

Voting for the Royal Society of Chemistry 2019 elections is now open and you should have been notified.

This year, they are holding elections for the following positions:

• RSC President (one vacancy)
• Elected Trustees (three vacancies)
• Elected member of Professional Standards Board (one vacancy)
• President of Analytical Division (one vacancy)
• President of Chemistry Biology Interface Division (one vacancy)
• President of Education Division (one vacancy)
• President of Environment, Sustainability and Energy Division (one vacancy)
• Elected member of Analytical Division Council (two vacancies)
• Elected member of Education Division Council (two vacancies)
• Elected member of Environment, Sustainability and Energy Division Council (two vacancies)
• Elected member of Faraday Division Council (two vacancies)
• Elected member of Materials Chemistry Division Council (two vacancies)
• Elected member of Organic Division Council (two vacancies)

Voting closes at 17:00 (UK time) on Friday 21 June 2019 so I'd urge you to vote ASAP.

On a personal note.

David Rees is standing for RSC President, I've known David for many years and I can't think of a better person to lead the RSC in these uncertain times. A really top class scientist with an excellent career in Drug Discovery, whilst maintaining contacts with academic research and holding important roles within the RSC.

 

Meetings for 2019 that CICAG (http://www.rsccicag.org) is involved with.

Workshop on Computational Tools for Drug Discovery (with SCI).
10 April 2019, The Studio, Birmingham.
https://www.soci.org/events/scirsc-workshop-on-computational-tools-for-drug-discovery A great opportunity to gets hands on training to get you started on a variety of important software tools. All software and training materials required for the workshop will be provided for attendees to install and run on their own laptops and use for a limited period afterwards.

Eighth Joint Sheffield Conference on Chemoinformatics, The Edge, University of Sheffield, UK, Monday 17th – Wednesday 19th June, 2019..
https://cisrg.shef.ac.uk/shef2019/ CICAG are really delighted to be sponsoring this meeting.

AI in chemistry (with RSC-BMCS).
Two-day meeting to be held in Cambridge on 2nd and 3rd September 2019. Fitzwilliam College
https://www.maggichurchouseevents.co.uk/bmcs/AI-2019.htm First very successful meeting in London was heavily oversubscribed, closing date for oral abstracts is 31 March and Posters 5 July.

Post-grad Cheminformatics/CompChem symposium, Wednesday 4th Sept 2019 Cambridge Chemistry Dept.
Opportunity for Post-grads to meet and present their work. Keep the date free, meeting details to be published soon, Cambridge Cheminformatics Network meeting will immediately follow the meeting so why not make a day of it.

20 years of Ro5 (with RSC-BMCS).
Wednesday, 20th November 2019, Sygnature Discovery, BioCity, Nottingham, UK.
It has been over 20 years since Lipinski published his work determining the properties of drug molecules associated with good solubility and permeability. Since then, there have been a number of additions and expansions to these “rules”. There has also been keen interest in the application of these guidelines in the drug discovery process and how these apply to new emerging chemical structures such as macrocycles. This symposium will bring together researchers from a number of different areas of drug discovery and will provide a historical overview of the use of Lipinski’s rules as well as look to the future and how we use these rules in the changing drug compound landscape. Details will be on https://www.maggichurchouseevents.co.uk/bmcs/ in the near future.

 

Registration opened just before Christmas and apparently there were a number of people sign up over the festive period. Remember there are a limited number of places and it is first come first served.

Registration and full details are here.

This workshop is intended to provide expert tutorials to get you started and show what can be achieved with the software.

 

In many companies/institutions/universities new arrivals are presented with a variety of desktop tools with little or no advice on how to use them other than "pick it up as you along". This workshop is intended to provide expert tutorials to get you started and show what can be achieved with the software.

The tutorials will be given a series of outstanding experts Christian Lemmen (BioSolveIT), Akos Tarcsay (ChemAxon), Giovanna Tedesco (Cresset), Dan Ormsby (Dotmatics) Greg Landrum (Knime ) and Matt Segall (Optibrium), you will be able to install the software packages on you own laptops together with a license to allow you to use it for a limited period after the event.

Registration and full details are here.

 

Royal Society of Chemistry members will be getting their annual subscription details around now. Can I remind people that your membership entitles you to membership of up to THREE Interest Groups. Apparently only around 25% take advantage of this option so I'd urge you to have a look at the groups available

In particular I'd like to highlight:-

86 Chemical Information and Computer Applications Group

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community, and to meet the requirements of the RSC’s strategy and charter. The storage, retrieval, analysis and preservation of chemical information and data are of critical importance for research, development and education in the chemical sciences. All chemists, and everybody else who works with chemical substances, need tools and techniques for handling chemical information.

If you have already submitted your form you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141).

If you want to find out more about CICAG activities the newsletters are available here and if you have ideas for future activities feel free to contact the committee.

 

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Group. The new website is now live, http://www.rsccicag.org

Why not have a browse around and let us know what else you would like to see included.

 

The new RSC CICAG website is now live http://www.rsccicag.org why not have a look and provide suggestions and feedback.

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community.

Also provides links to the social media feeds (Twitter, LinkedIn etc.)

 

The Winter 2017-18 edition of the CICAG Newsletter has been published and can be downloaded from the Newsletters webpage.

Features in this edition which may be of interest include: * Details of CICAG's upcoming Artificial Intelligence in Chemistry meeting * 30th Anniversary celebration of the Catalyst Science Discovery Centre and a look at the scientific history and achievements of the area * Tony Kent Strix Award and Annual Lecture 2017 and eLucidate from UKeiG * Other CICAG planned and proposed meetings along with other upcoming conferences and events * Meeting reports * Book reviews * News from Infochem and CAS * A review of the latest chemical information news and developments

PhD Student and Post-Doc Conference Bursaries

Did you know that most CICAG sponsored meetings have a number of bursaries available for PhD and post-doctoral students? Normally up to a value of £250, these awards help to cover registration and travel costs. Preference will be given to members of the RSC (and meeting co-sponsors if applicable), especially those who are selected to give posters.

RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Friday, 15th June 2018 Royal Society of Chemistry at Burlington House, London, UK. Twitter hashtag - #RSC_AIChem

 

If you are a Royal Society of Chemistry member renewing your annual mebership, can I remind you that your membership entitles you to membership of up to THREE Interest Groups. Apparently only around 25% take advantage of this option so I'd urge you to have a look at the groups available.

In particular

86 Chemical Information and Computer Applications Group

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community, and to meet the requirements of the RSC’s strategy and charter.

If you have already submitted your form you can make a request to join a group via email (membership@rsc.org) or telephone (01223 432141).

The first announcement of a CICAG/BMCS meeting to be held next year.

RSC-BMCS / RSC-CICAG Artificial Intelligence in Chemistry Friday, 15th June 2018 Royal Society of Chemistry at Burlington House, London, UK.
Twitter hashtag - #RSC_AIChem

 

Royal Society of Chemistry members will be getting their annual subscription details around now. Can I remind people that your membership entitles you to membership of up to THREE Interest Groups.

I'd urge you to make use of them, in particular:-

86 Chemical Information and Computer Applications Group

Update

Currently it seems Members who wish to change/join interest groups and divisions currently need to request this via email (membership@rsc.org) or telephone (01223 432141).

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups, which exist to benefit RSC members and the wider chemical science community, and to meet the requirements of the RSC’s strategy and charter.

Scope and Aims

The storage, retrieval, analysis and preservation of chemical information and data are of critical importance for research, development and education in the chemical sciences. All chemists, and everybody else who works with chemical substances, need tools and techniques for handling chemical information.

CICAG works to:

• Support users of chemical information, data and computer applications and advance excellence in the chemical sciences
• Inform RSC members and others of the latest developments in these rapidly evolving areas
• Promote the wider recognition of excellence in chemical information and computer applications at this level.

CICAG also organises a number of meetings each year at which members get reduced rates. Details of previous meetings are here.

You can also follow CICAG on Twitter https://twitter.com/RSC_CICAG or LinkedIn https://www.linkedin.com/groups/1989945.

 

The 2017 Summer Newsletter is now available for download.

This includes reports from the scientific meetings supported, and details of potential future meetings, together with news items that might be of interest to members of RSC CICAG interest group.

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups.

The aims of the group are:-

• support users of chemical information, data and computer applications and advance excellence in the chemical sciences
• inform  RSC members and others of the latest developments in these rapidly evolving areas;
• promote the wider recognition of excellence in chemical information and computer applications at this level.

If you are an RSC member who is interested in joining the group contact the membership team

 

UKeiG presents the Tony Kent Strix Award in partnership with the International Society for Knowledge Organisation (ISKO UK) and the British Computer Society Information Retrieval Specialist Group (BCS IRSG). The award is sponsored by the Royal Society of Chemistry Chemical Information & Computer Applications Group.

The UK electronic information Group (UKeiG) is now seeking 2017 nominations for this prestigious award.

The Tony Kent Strix Award is given in recognition of an outstanding practical innovation or achievement in the field of information retrieval in its widest sense, including search and data mining, for example. This could take the form of an application or service, or an overall appreciation of past achievements from which significant advances have emanated. The award is open to individuals or groups from anywhere in the world.

The deadline for nominations is Thursday 31st August 2017.

Nominations should be for achievement that meets one or more of the following criteria:

• A major and/or sustained contribution to the theoretical or experimental understanding of the information retrieval process
• Development of, or significant improvement in, mechanisms, a product or service for the retrieval of information, either generally or in a specialised field
• Development of, or significant improvement in, easy access to an information service
• Development and/or exploitation of new technologies to enhance information retrieval
• A sustained contribution over a period of years to the field of information retrieval for example, by running an information service or by contributing at national or international level to organisations active in the field.

Key characteristics that the judges will look for in nominations are innovation, initiative, originality and practicality.

The information to be supplied in the nomination should comprise:

• The name, institutional address and qualifications of the nominee
• A brief biography (not more than one page of A4)
• A relevant bibliography (i.e. not comprehensive but including the key publications relevant to the nomination)
• A justification for the nomination, of not more than one page of A4, showing clearly which of the Strix award criteria the nominee meets and how the criteria are met
• Additional material (e.g. letters of support - letters from past winners would be especially valuable).

It is possible that the Award Committee will request additional information from the nominators for those nominees considered suitable candidates for the award.

Nominations for the 2017 award should reach the judges by Thursday August 31st 2017 and be emailed to:

John Wickenden – Hon. Secretary UKeiG secretary.ukeig@cilip.org.uk
cc-ed to Gary Horrocks - UKeiG administrator admin@ukeig.org.uk
cc-ed to Sue Silcocks – Hon. Treasurer UKeiG treasurer.ukeig@cilip.org.uk

 

The Royal Society of Chemistry Chemical Information and Computer Applications Group (CICAG) are conducting a survey to find out more about the way that scientists use the various social media channels.

The survey is very short and feedback would be appreciated from everyone, you don't have to be a member of the RSC (or CICAG) to contribute.

The survey can be found here https://www.surveymonkey.co.uk/r/YSYFRDP.

The Chemical Information and Computer Applications Group (CICAG) is one of the RSC’s many member-led Interest Groups.

 

The Royal Society of Chemistry Twitter Poster Conference is an online event held entirely over Twitter to bring members of the scientific research community together to share their research, network and engage in scientific debate. Building upon the success of the previous two Analytical Science Twitter Poster Conferences, the 2017 poster conference encompassed all areas of the chemical sciences. The conference reached the scientific research community around the world, achieving 1,650 contributors, 6,473 tweets, an audience of 2,770,749 and 11,841,519 total impressions.

 

Royal Society of Chemistry members will be getting their annual subscription details around now. Can I remind people that your membership entitles you to membership of up to THREE Interest Groups. I'd urge you to make use of them, in particular:-

33 Biological and Medicinal Chemistry Sector
86 Chemical Information and Computer Applications Group.

Reduced subscription rates are also available to:

Full time postgraduate students (including PGCE students) – £19 Low income members with an income below £26,000 per annum – Fellow £74, Member £65, Associate £39, Affiliate £41 Retired members – Fellow £74, Member £65, Associate £39, Affiliate £41

 

Here is the meeting report for the Chemistry on Mobile Devices: Create, Compute, Collaborate conference that was held yesterday. Organized by RSC CICAG.

Mobile devices are now ubiquitous, there are now estimated to be over two billion SMART phones and tablets in use globally. Each with the computing power to handle most of a chemists needs. The aim of the meeting was to look at the many ways that mobile devices could become the chemist’s essential companion. From searching and consuming content, to performing computational calculations and providing interactive visualizations. From electronic notebooks to devices accessing Cloud based resources.

Nice of Apple to chose to release the iPhone 7 after the meeting :-)

 

An interesting conference organised by RSC Chemical Information and Computer Applications Group 7 September 2016 10:00-16:30, Cambridge, United Kingdom

Mobile devices are now ubiquitous: there are estimated to be over two billion smart phones and tablets in use globally, each with the computing power to handle most of a chemist's needs. The meeting will explore the many ways that mobile devices could become the chemist's essential companion, from consuming content to performing computational calculations, from electronic notebooks to devices accessing cloud-based resources, and much more.

More details

http://www.rsc.org/events/detail/22602/chemistry-on-mobile-devices-create-compute-collaborate

 

The RSC's Undergraduate Research Bursaries are now open for 2016 entries, seeking talented chemical sciences students to undertake a research placement this summer.

These research bursaries are to fund short (6-8 weeks) summer research projects for undergraduate chemistry students in the middle years of their course. The purpose of the awards is to give experience of research to undergraduates with research potential and to encourage them to consider a career in scientific research.

The bursary is worth £200 per week (£210 in London) for up to 8 weeks to cover a defined research placement.

The deadline for applications is 21 February 2016.

Please note that, for the first time, in 2016 CICAG will be funding one student bursary for research work which falls into one or more of the following areas: cheminformatics, chemical information, chemical data management, chemistry data analytics, applications of computational chemistry.

For more information about guidelines, eligibility criteria, award conditions, and the application form please see the Undergraduate Research Bursaries web page http://www.rsc.org/Education/HEstudents/undergraduate-bursary.asp

Any questions should be directed to the Under Graduate Bursaries team (see link on the Undergraduate Research Bursaries web page linked to above).

 

If you are renewing your Royal Society of Chemistry subscription remember your membership covers up to three interest groups. If you are interested in cheminformatics you might be interested in the Chemical Informations and Computer Applications group.

I'm on the committee and we have a couple of interesting meeting in the planning stage.

 

An interesting meeting for anyone who is interested the storing, exchange of chemicals, names or identifiers.

What’s in a Name:  Terminology and Nomenclature the unsung heroes of open innovation

21st October 2014
CICAG and ITaaU one Day Meeting
RSC, Burlington House, London

Introduction & Keynote
10.00 Registration and tea/coffee
10.30 Welcome. Representative from the Royal Society of Chemistry
10.40 Introduction. Jeremy Frey, University of Southampton

10.45 Keynote presentation: What's in a Name? Possibly Death and Taxes! Richard Hartshorn, University of Canterbury, Christchurch, New Zealand; Past President, IUPAC Division of Chemical Nomenclature and Structure Representation

Nomenclature Challenges for the 21st Century
11.25 Extended Structures, Crystallography and Polymers – Challenges. Clare Tovee, Cambridge Crystallographic Data Centre
11.45 Naming Polymers – Buy One Get One Free. Richard Jones, Emeritus Professor of Polymer Science, University of Kent; UK National Representative, IUPAC Polymer Division
12.05 The Importance of Chemical Identifier Standards in the Pharmaceutical Industry. Colin Wood, Enterprise Information Architect, R&D IT, GlaxoSmithKline
12.25 Discussion
12.45 Lunch

The Impact of Computers and the Web
13.30 The Web – What is the Issue? Egon Willighagen, Department of Bioinformatics, Maastricht University
13.50 Health and Safety and the Semantic Web. Mark Borkum, Department of Chemistry, University of Southampton
14.10 Defining Chemical Classes in OWL-based English for ChEBI. Janna Hastings, EBI
14.30 The IUPAC Green Book – Unit's Dictators Source Book? Jürgen Stohner, Zürich University of Applied Sciences; IUPAC Commission on Physicochemical Symbols, Terminology, and Units (Comm. I.1)
14.50 Reaction InChI – Distilling the Essence of a Chemical Transformation. Jonathan Goodman, University of Cambridge and Jeremy Frey, University of Southampton
15.10 Discussion
15.30 Tea/coffee

15.50 Keynote presentation: From Chaos Comes Order – Managing Data in Open Source Drug Discovery. Matthew Todd, University of Sydney

16.30 Discussion and RSC/CICAG Role
16.50 Meeting closes