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.

 

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

 

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

 

The playlist for the RSC CICAG Open Source tools for Chemists workshops has been updated. There are now 11 two hour videos covering a wide variety of tools from data analysis, docking, molecular visualisation, fragment screening etc. These videos have now been watched over 6000 times and have attracted significant praise.

Two hours of distilled pure science.

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

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.

 

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 next RSC CICAG Open Source tools workshop is on 24 June and highlights DataWarrior, it will be given by Isabelle Giraud.

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.

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) 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 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.

 

Save the dates. More details coming soon on this virtual workshop.

MSSC2021 - Ab initio Modelling in Solid State Chemistry
Virtual Edition (New Users)
Discovering quantum-mechanical simulations with CRYSTAL
London (UK time), September 20-24,2021
Directors: S. Casassa - A. Erba - N.M. Harrison - G. Mallia

The week long school is designed for new users of CRYSTAL, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide an introduction to the capabilities of quantum mechanical simulations and to the practical use of CRYSTAL.

CRYSTAL is a general-purpose program for the study of periodic systems. The code may be used to perform consistent studies of the physical and chemical properties of crystalline solids, surfaces, polymers, nanotubes and molecules. The CRYSTAL program computes the electronic structure, structural features, vibrational, magnetic, dielectric (linear and non-linear electric susceptibilities up to forth-order), elastic, piezoelectric, photoelastic, thermodynamic (Quasi-Harmonic Approximation) and transport properties of periodic systems, within Hartree Fock, density functional or various hybrid approximations (global and range-separated hybrids).

CRYSTAL17 for Unix/Linux/MacOSX is supplied as binary executables or object files for a number of supported architectures. Precompiled executables include sequential (crystal, properties) and replicated data parallel version (Pcrystal). The massive parallel version (distributed memory, MPPcrystal) is only supplied as object files

 

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 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

 

Over the years RSC CICAG have held workshops providing tuition for various software packages, because of the physical limitations these workshops had to be limited to around 50 attendees leaving us with a waiting list of folks who missed out. Because of the COVID-19 pandemic the meetings have been moved online allowing much greater access. The recent Open Chemical Science workshops had attendees from 45 different countries. There was considerable interest in including further workshops and so CICAG have started a monthly workshop series, each month a workshop will be held highlighting a particular package/resource.

The first four workshops are now organised, you can register here. These look to be very popular with registrations already up to 150 for the first workshop, which is three-fold higher than we could have accommodated in a physical workshop.

There are four two-hour sessions in this series which will be run on Zoom.

• 25th March ChimeraX (https://www.rbvi.ucsf.edu/chimerax/) from Tom Goddard Intro to ChimeraX for visualizing proteins, ligands and X-ray and electron microscopy maps. Install ChimeraX beforehand (https://www.rbvi.ucsf.edu/chimerax/) and follow along as we look at nanobody binding to SARS-CoV-2 spikes (https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/nanobody.html).

• 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. This workshop will use Python and Jupyter notebooks, delegates will need to install Jupyter and RDKit best installed using conda https://www.rdkit.org/docs/Install.html#cross-platform-under-anaconda-python-fastest-install.

• 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/.

These workshops are sponsored by LiverpoolChiroChem.

The previous workshops are now available on the RSC CICAG YouTube channel.

 

Last year RSC CICAG held a five day conference entitled Open Chemical Science this online event proved to be enormously popular with attendees from 45 different countries. One feature of the meeting was a series of workshops highlighting a number of open-source software tools, these workshops are now available on the RSC CICAG YouTube channel.

There was considerable interest in including further workshops and so CICAG have started a monthly workshop series, each month a workshop will be held highlighting a particular package/resource.

The first four workshops are now organised, you can register here.

There are four two-hour sessions in this series which will be run on Zoom.

• 25th March ChimeraX (https://www.rbvi.ucsf.edu/chimerax/) from Tom Goddard Intro to ChimeraX for visualizing proteins, ligands and X-ray and electron microscopy maps. Install ChimeraX beforehand (https://www.rbvi.ucsf.edu/chimerax/) and follow along as we look at nanobody binding to SARS-CoV-2 spikes (https://www.rbvi.ucsf.edu/chimerax/data/nanobody-feb2021/nanobody.html).

• 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. This workshop will use Python and Jupyter notebooks, delegates will need to install Jupyter and RDKit best installed using conda https://www.rdkit.org/docs/Install.html#cross-platform-under-anaconda-python-fastest-install.

• 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/.

 

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

 

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.