Macs in Chemistry

Insanely Great Science

Tutorials

RSC CICAG workshops

 

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

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RSC CICAG YouTube playlist

 

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

Screenshot 2021-07-27 at 09.46.12

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.

Comments

OPIG (Oxford Protein Informatics Group) antibody modelling tools workshop

 

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.

Comments

More RSC CICAG workshops

 

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.

DataWarrior2

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.

Comments

Using JDBC Driver to access Athena from Vortex

 

This tutorial is a step by step guide to access data in Athena from Vortex.

Amazon Athena is an interactive query service that makes it easy to analyze data in Amazon S3 using standard SQL. Athena is serverless, so there is no infrastructure to manage, and you pay only for the queries that you run. Athena is easy to use. Simply point to your data in Amazon S3, define the schema, and start querying using standard SQL. Most results are delivered within seconds. With Athena, there’s no need for complex ETL jobs to prepare your data for analysis. This makes it easy for anyone with SQL skills to quickly analyze large-scale datasets.

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RSC CICAG YouTube channel

 

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.

CICAGYoutube

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Open-Source Tools for Chemistry Workshops

 

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.

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.

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Open-Source Tools for Chemistry Workshops

 

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.

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/.

Comments

Unix tips for dealing with very large files

 

I've updated the page describing a variety of unix commands that can be helpful when dealing with very large files. In particular I've added details of how to split very large files into more manageable chunks.

Dividing sdf files can be problematic since we need each division to be at the end of a record defined by "$$$$". I've spent a fair amount of time searching for a high-performance tool that will work for very, very large files. Many people suggest using awk

AWK (awk) is a domain-specific language designed for text processing and typically used as a data extraction and reporting tool. Like sed and grep, it's a filter, and is a standard feature of most Unix-like operating systems.

I've never used awk but with much cut and pasting from the invaluable Stack Overflow this script seems to work.

awk -v RS='\\$\\$\\$\\$\n' -v nb=1000 -v c=1 '
{
  file=sprintf("%s%s%06d.sdf",FILENAME,".chunk",c)
  printf "%s%s",$0,RT > file 
}
NR%nb==0 {c++}
' /Users/username/Desktop/SampleFiles/HitFinder_V11.sdf

The result is shown in the image below. There are a couple of caveats, this script only works with the version of awk shipped with Big Sur (you should be able to install gawk using Home Brew and use that on older systems), and it requires the file has unix line endings. The resulting file names is not ideal and if there are any awk experts out there who could tidy it up I'd be delighted to hear from you.

awkresults

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Open Chemical Sciences Workshops

 

The RSC CICAG Open Chemical Sciences meeting was a great success with attendees from around the world able to attend this online event. You can read more about the meeting on the CICAG website http://www.rsccicag.org/previous%20meetings.htm.

One component of the meeting was a series of workshops highlighting key Open-Source software applications for chemists. These sessions were recorded and are now available on the CICAG YouTube channel.

DataWarrior workshop by Isabelle Giraud 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. This workshop is an introductory tutorial, DataWarrior can be downloaded here http://www.openmolecules.org/datawarrior/download.html.

PyMOL workshop by Garrett Morris PyMOL is a comprehensive software package for rendering and animating 3D structures, in particular biomolecules. Website https://pymol.org/2/ You can 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/ or PyMOL from GitHub: https://github.com/schrodinger/pymol-open-source

UsingGoogleCoLab workshop by Jan Jensen Colaboratory, or "Colab" for short, allows you to write and execute Python in your browser, with Zero configuration required.

  • Initial notebook: https://colab.research.google.com/drive/1t2ED9woH_cTOhCiiUZZzrTIUUfwsSds5?usp=sharing
  • Final notebook: https://colab.research.google.com/drive/1rJOE6RNTCjByMqR-L3B7tZtwML3nIQVf?usp=sharing

ChEMBL workshop by Anna Gaulton ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.. This workshop is an introductory tutorial. Website https://www.ebi.ac.uk/chembl/

Fragalysis workshop by Rachel Skyner Fragalysis (fragment analysis) is a web-based platform for fragment-based drug discovery https://fragalysis.diamond.ac.uk/viewer/react/landing/). It’s initial use case is focussed around the fragment screening experiment at Diamond.. This workshop is an introductory tutorial.

Knime workshop by Greg Landrum 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. This workshop is an introductory tutorial. Knime can be downloaded here https://www.knime.com/downloads. Data used in tutorial are here


Comments

Learn Fortran

 

I just heard about a series of online mini-books on learning Fortran Learn Fortran, and I've added them to the Fortran on a Mac page.

They start with how to install Fortran and go onto a tutorial about the syntax and building your own programs.


Comments

Introductory video for iNMR

 

Giuseppe Balacco has posted an introductory video that shows many basic operations applied to a simple 1-H spectrum using iNMR

If you have any comments or suggestions I'm sure Giuseppe would be delighted to see them posted on the YouTube page.

iNMR is the software of your dreams: elegant yet affordable, straightforward yet complete, tightly integrated with the OS, well tested and fast. When your spectra are beautifully reproduced in full screen size and they respond immediately to your commands, that is the ultimate NMR experience! iNMR can do all the things you expect from a traditional NMR program (and ten times more), plus the things you would expect from a genuine Mac or Win application. The clean interface is the secret to the high user satisfaction and productivity. iNMR is being continuously updated and tailored to the needs of the customers. One-to-one support and tailored programming are included.

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Determining the Amino Acids in a collection of peptides

 

I've recently become interested the comparison of the amino amino-acid composition of peptides, to allow comparison of cyclic versus linear peptides, or brain penetrant curses non-penetrant. I had a look around but could not find any tools that did this, in particular I wanted to include any non-proteinergic amino-acids.

This tutorial provides a means to analyse many thousands of peptides using Vortex.

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Adding substructure searching to a FileMaker Pro Database

 

Anyone who has had to store or search a collection of chemical structures rapidly realises that they need a software tool with a little chemical intelligence. Whilst there are a number of commercial databases they tend to be rather expensive and often require a knowledge of SQL or dedicated IT support. Fine for large corporations but not suitable for a single chemist or small group. In contrast FileMaker Pro is a popular desktop database with an easy to use interface (there are also server and mobile versions). Unfortunately whilst it is easy to use it does not support chemical structure based searching. Fortunately FileMaker Pro comes with an easy to use scripting interface and we can create scripts that run command line applications like Openbabel.

Findlistsearch

This tutorial shows how to add substructure and similarity searching to a FileMaker Pro database, full details are available here including download of example database.

Comments

Counting Identical structures in two datasets

 

Sometimes I have two datasets and I just want to know the overlap of identical structures. This Vortex script counts the number of identical structures by comparing InChIKeys. It then displays a matrix showing how many unique molecules in each dataset and how many molecules are in both datasets.

results

Comments

SCI-RSC Workshop on Computational Tools for Drug Discovery

 

I'm delighted to report this meeting seems to be filling up fast

All scientists working in drug discovery need tools and techniques for handling chemical information. This workshop offers a unique opportunity to try out a range of software packages for themselves with expert tuition in different aspects of pre-clinical drug discovery. Attendees will be able to choose from sessions covering data processing and visualisation; ligand and structure-based design, or ADMET prediction run by the software providers. 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

More details

Presentations from Optibrium / Cresset / Dotmatics /BioSolveIT/ Knime / ChemAxon

Comments

Workshop on Computational Tools for Drug Discovery

 

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.

Computational Tools Flyer

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

Comments

Rescoring Docking using RF-Score-VS

 

A little while back I described a docking workflow including a rescoring script for Vortex, so I thought it might be useful to include this on a separate page.

Recently, machine-learning scoring functions trained on protein-ligand complexes have shown significant promise an example being (RF-Score-VS) trained on 15 426 active and 893 897 inactive molecules docked to a set of 102 targets DOI.

Our results show RF-Score-VS can substantially improve virtual screening performance: RF-Score-VS top 1% provides 55.6% hit rate, whereas that of Vina only 16.2% (for smaller percent the difference is even more encouraging: RF-Score-VS top 0.1% achieves 88.6% hit rate for 27.5% using Vina). In addition, RF-Score-VS provides much better prediction of measured binding affinity than Vina (Pearson correlation of 0.56 and −0.18, respectively). Lastly, we test RF-Score-VS on an independent test set from the DEKOIS benchmark and observed comparable results.

Binaries for RF-Score-VS are available https://github.com/oddt/rfscorevs_binary.

results.png

The full details of the Vortex script are here.


Comments

Workshop on Computational Tools for Drug Discovery

 

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.

Computational Tools Flyer



Comments

Making a Random Selection

 

Sometimes it is the simplest scripts that prove to be the most useful, the most downloaded AppleScript on the site is the one that simply prints the text on the clipboard.

I regularly need to select a specified number of molecules in a random fashion and this script does just that. Import a sdf file containing structures into Vortex and run the script to make a random selection.

results

Full details here….


Comments

Intelligently Automating Machine Learning, Artificial Intelligence, and Data Science

 

A timely tutorial and example workflow.

we have put together a more comprehensive workflow, serving as a blueprint for anyone to build her or his own version of a Guided Analytics application to combine just the right amount of automation and interaction for a specific set of problems.

Full details here


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Tips & Tricks for Using KNIME

 

The Knime blog has a post containing lots of user submitted tips and tricks

Ever sat next to a friend or colleague at the computer and were awed when you suddenly realised the way they do certain tasks is much better? We recently asked KNIME users to share their tips and tricks on using KNIME. In this series of posts we’ll be showing you how the experts use KNIME in the hopes that by sharing ideas you’ll discover some handy techniques.


Comments

Updated Literature search script

 

I've updated the Vortex script to run text based queries of PubMed.

If you regularly use the E-utilities API you might want to read this.

After May 1, 2018, NCBI will limit your access to the E-utilities unless you have one of these keys. Obtaining an API key is quick, and simple, and will allow you to access NCBI data faster. If you don’t have an API key, E-utilities will still work, but you may be limited to fewer requests than allowed with an API key.

After May 1, 2018, any computer (IP address) that submits more than 3 E-utility requests per second will receive an error message. This limit applies to any combination of requests to EInfo, ESearch, ESummary, EFetch, ELink, EPost, ESpell, and EGquery.

If you write software of scripts that access the E-utilities API then the users will need to get their own api key. Calls will have this format

https://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed&api_key=ABCD123

I've updated this script to reflect this change, and I've highlighted where you need to add your api key in the script. I've also tried to ensure that any query string should be encoded to make it URL safe and I've extended the search range up to 2018.

AIsearchresults


Comments

Flagging Potential Kinase Inhibitors

 

Most of kinase inhibitors bind in the region of the ATP binding site using the hydrogen bonding interactions of the hinge region shown in the schematic below. We can use the knowledge of these hinge binding motifs to flag potential kinase inhibitors.

schematicatpbinding

Read more ….


Comments

Scripting PubMed searches

 

PubMed comprises more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. They also provide a number of programming tools that allow access to the information, E-utilities are a set of server-side programs that provide a stable interface into the Entrez query and database system.

To access these data, a piece of software first posts an E-utility URL to NCBI, then retrieves the results of this posting, after which it processes the data as required. The software can thus use any computer language that can send a URL to the E-utilities server and interpret the XML response; examples of such languages are Perl, Python, Java, and C++.

A while back I wrote a vortex script that helps with these sort of searches if you have multiple terms you want to search. I've updated this script to incorporate the changes requiring api keys to allow multiple requests to the E-utilities api, and I've highlighted where you need to add your own api key in the script. I've also tried to ensure that any query string should be encoded to make it URL safe.

The update is detailed more fully here….

tut25result


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Interacting with the RCSB Protein Data Bank

 

The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease. Currently the PDB contains over 134,000 data files containing structural information on 42547 distinct protein sequences of which 37600 are human sequences. They also provide a series of tools to search, view and analyse the data.

The latest addition to the Hints and Tutorials page is a couple of Vortex scripts for interacting with the RCSB Protein Data Bank, specifically they search for PDB structures associated with a list of Uniprot codes, and then search for associated information. Read more here…

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Predicting sites of metabolism Vortex script

 

It is really useful to have two sites of metabolism tools available that use contrasting methodologies, FAME 2 using curated dataset of experimentally determined metabolism data to build a machine learning model using simple descriptors. In contrast SMARTCyp uses precomputed activation energies from density functional theory (DFT) calculations of model compounds.

I previously wrote a script displaying the [results of a SMARTCyp calculation in a webview. The first part of the script imports the smartcyp.jar, however with each update I was finding issues so I thought it might be better to simply treat SMARTCyp as a command line application and use subprocess to access it.

Using a similar script we can also access FAME2

More details here.

somprediction


Comments

Dealing with Greek characters in column names

 

This is just a very quick tip when dealing with Greek characters in Vortex column names when creating a script. It may be obvious to many but I struggled for several hours before finding the problem and a solution

Read more…


Comments

Flexible UniChem Search

 

UniChem is a web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases. Currently the UniChem contains data from 27 different data sources. Currently UniChem provides links to 108,941,995 structures.

Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3

The previous script showed how to search using ChEMBLID, however one of the attractions of UniChem is that you can search with any molecule identifier if you know the corresponding datasource. This script allows the user to use any molecule identifiers and then search a specified datasource using a common web service.

Read more …


Comments

Getting UniChem data from ChEMBL

 

UniChem is a web resource provided by the EBI, it is a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases. Currently the UniChem contains data from 27 different data sources. Currently UniChem provides links to 108,941,995 structures.

Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3

ChEMBL also provide a RESTful Web service that users can use to retrieve data from the UniChem database in a programmatic fashion.

Read more…


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Installing Checkmol/Matchmol under Mac OSX

 

Checkmol is a command-line utility program which reads molecular structure files in different formats and analyzes the input molecule for the presence of various functional groups and structural elements. At present, approx. 200 different functional groups are recognized. Output can be either clear text (English or German), a bitstring or its ASCII representation, or a set of special 8-character codes. This output can be easily placed into a database table, permitting the creation of chemical databases with a functional group search option. It was written by Norbert Haider, Department of Pharmaceutical Chemistry (now: Department of Drug and Natural Product Synthesis), University of Vienna, Austria.

The software is available both as source code and as a binary compiled for Linux (x86 architecture). It is entirely written in Pascal and it was compiled with Free Pascal 1.0.11 or Free Pascal 2.4.0 (starting from v0.4c). So to install we first need to get a Pascal compiler, this can be downloaded from Sourceforge.

Full details are here.

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Importing Open Source Malaria Project data

 

The Open Source Malaria project is trying a different approach to curing malaria. Guided by open source principles, everything is open and anyone can contribute. To date a lot of people around the world have made contributions and the project is at a very exciting stage. Whilst everyone can see the compounds that have been made and the biological data, it is often spread over multiple web pages and can be tricky to link molecule with identifier with data. Over the last couple of months a significant effort has been put into populating a spreadsheet with all the information.

Whilst this is useful for viewing results it is not ideal for trying to build predictive models. Vortex is a chemically intelligent data analysis and visualisation platform. This script provides a one-click access to the OSM data and creates a workspace containing all the data, and since it is linked to the live spreadsheet you will always have access to the latest data.

osmvortex

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Scripting Vortex 25

 

Whilst most of the Vortex scripts mentioned on this site to date involve chemical structures we should not forget that Vortex is an excellent general data analytics tool and the data set does not have to include any molecular structures. Recently I was asked about the number of publications associated with a particular potential therapeutic target and it struck me that Vortex might actually be an excellent tool to investigate this.

Read More.

vorte25_1

Comments

Cheminformatics on a Mac

 

A little while back I wrote a detailed tutorial for getting a wide variety of cheminformatics tools running on a Mac.

Someone just let me know about an issue with OSRA a utility designed to convert graphical representations of chemical structures, as they appear in journal articles, patent documents, textbooks, trade magazines etc., into SMILES

It turns out that OSRA requires ghostscript to process pdf images, this can be installed using brew.

brew install ghostscript
Comments

MedChem Wizard KNIME workflow

 

The MedChemWizard is a KNIME workflow designed to assist medicinal chemists with idea generation, ligand design and lead optimization using a number of common functional group transformations and medchem rules-of-thumb, this tutorial provided by Dr. Alastair Donald gives a detailed description of it's use.

mcwizard

Comments

BBEdit tutorial

 

I'm a long time BBEdit user but I still enjoy reading tips for making your use of BBEdit more efficient.

This blog post offers some tips for the various "Find" options within BBEdit.

I'd certainly agree with the final comment.

Text editors with limited capabilities keep you at a beginner level, no matter how long you've been using them. Serious text editors have a depth that rewards their users.

Comments

Bringing Open Source to Drug Discovery

 

I gave a talk at the RSC 25th Symposium on Medicinal Chemistry in Eastern England meeting last week entitled “Bringing Open Source to Drug Discovery”.

The slides and pages of links are available here.

I also captured the laptop screen of the demo which I’ve now put on YouTube.

https://www.youtube.com/watch?v=sG9vDIfp0NE&feature=youtu.be

The aim was to show what was available and to show how they can be integrated into proprietary tools using scripting, many of the scripts are available on the hints and tutorials page.


Comments

Scripting Vortex 12

In the previous tutorial we made use of the Virtual Computational Chemistry Laboratory web service to calculate aLogP and LogS, both these results were returned in a simple text format. More recently there has been an increased use of JSON format for data exchange.

JSON, or JavaScript Object Notation, is a text-based open standard designed for easy human-readable data interchange. It is derived from the JavaScript scripting language for representing simple data structures and associative arrays, called objects. Despite its relationship to JavaScript, it is language-independent, with parsers available for many languages including including C, C++, C#, Java, JavaScript, Perl, Python.

Molinspiration provide a number of cheminformatics tools but also provide a RESTful web service these web services can be used to calculate a range of molecular properties and bioactivity predictions.

The output from both web services is available either as a JSON string or plain text, the web service can be accessed by submitting a URL

Full details of the script are here.

vortex1