Macs in Chemistry

Insanely Great Science

A Functional Group Count Script

 

I recently wrote a review of Reaction Workflows, a web-based tool that allow users to build workflows from nodes that provide inputs and outputs or perform actions, including ones to perform reaction-, scaffold-, and transform-based enumeration, and it is all done within a web browser interface using drag and drop. Whilst you can draw input structures one of the real strengths is the ability to import pre-categorised reagent files e.g.Acid Chlorides or secondary amines. This script is intended to help with this within Vortex.

This script is a variation of the high performance sub-structure search scripts described previously, however instead of simply flagging the presence (or absence) of a SMARTS query we provide a count of the number of times a SMARTS query is identified within a molecule. The script uses all available cores and is thus capable of running multiple queries in parallel and can thus handle very large datasets. The script currently contains around 70 different SMARTS queries for both functional groups and atom counts and I'd be happy to add any suggestions.

Read more….


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Getting PDB information

 

A while back I published two scripts that use UniChem a web resource provided by the EBI, a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases.

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 first script uses the ChEMBL ID to search for other identifiers, the second script allows more flexible searching using any of the identifiers available within UnicChem. One of the identifiers returned is from the PDBe (Protein Data Bank Europe) and represents the ID of the ligand in the PDB. Whilst this is interesting it would also be very useful to have the identity of the crystal structures that contain the ligand. Fortunately PBDe provide a series of web services that can be used to interrogate the database, together with a really useful page to help build the calls.

Full details of the script are here..

There is a comprehensive listing of scripts, tips, jupyter notebooks etc here.


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Several ways of scripting Name to Structure

 

Too often I come across datasets that Chemical names or identifiers but no actual molecular structure, recently Dan at Dotmatics suggested I look at OPSIN. There are also several web services for converting names to structure and I've highlighted a couple of options here and described three scripts that allow them to be used from within Vortex.

vortexopsinstructures.png

There are many more scripts on the Hints and Tutorials Page.


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Vortex does Biology

 

I was at the Dotmatics UGM recently and they gave an insight into some of the future directions. One of the areas under consideration is the use of Vortex support for Biological data analysis.

Vortex is a very high performance data analysis and plotting tool, capable of handling many millions of rows of data. It also has chemical intelligence built in, allowing structure-based searching, physicochemical properties calculation, clustering and match pair analysis.

The support for biology is a new addition and I've written a brief review here.

sequaligned

Added to the growing list of software reviews.


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Scripting Vortex 34, analysis of catagorical information

 

I often need to tag individual molecules within a dataset with a specific property, perhaps the results of clustering algorithms, the results of PAINS filtering, or Liver toxicity filters. Alternatively if you have a drug discovery project with multiple chemotypes you might want to tag particular groups of compounds as belonging to a named series to aid analysis.

A question that might then arise is “How many molecules belong to each category?”. Whilst you can see the numbers in the sidebar there is not an easy way to export the results.

Hopefully this script can help.

livertoxoutput


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Accessing ZINC supplier information

 

ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 100 million purchasable compounds in ready-to-dock, 3D formats. Sterling and Irwin, J. Chem. Inf. Model, 2015. This is an invaluable resource for any type of virtual screening or for anyone looking to create a physical screening or fragment collection.

Once you have done the virtual screening you will rapidly realise that the really time-consuming a tedious part now lies ahead. Finding out which vendors stock a particular molecule and then ordering them. Looking up the vendor details for individual compounds is extremely tedious and so this Vortex script may be very useful.

Many more scripts, iPython notebooks and tutorials can be found here.


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Dotmatics UGM

 

Dotmatics User Group Meeting – Cambridge, UK
Churchill College, Cambridge, UK
Tuesday, 13 September 2016 at 09:00 - Wednesday, 14 September 2016 at 16:00 (BST)

Full details and agenda here


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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…


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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 …


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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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Finding Duplicate structures

 

It is always interesting to note which scripts attract the most attention, often it is scripts that aid with relatively simple tasks. Among the Applescripts it is the script to simply print the clipboard.

Recently I wrote a script to remove duplicate structures from within Vortex

When working with multiple data sets of molecules, particularly if combining them from multiple sources, one of the most common tasks is removal of duplicates. This can be a time-consuming and error prone process if carried out manually and this script should hopefully make this a much easier task.

This seems to have attracted interest but I got a comment that it "works fine but is slow for larger data sets". So I've been looking at improving performance.

In order to test the performance I took around 150,000 random structures from ChEMBL and then duplicated 0.01% to give a test set of 160,146 molecules. The original version of the script took 95 mins, using the same test set, version 2 of the script took less than 3 mins! This increase in performance means that it is now practical to use the script on much larger datasets.

You can read full details and download it here.

There are many more Hints, scripts and tutorials here.

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Script to remove duplicates in Vortex

 

When working with multiple data sets of molecules, particularly if combining them from multiple sources, one of the most common tasks is removal of duplicates. This can be a time-consuming and error prone process if carried out manually and this script should hopefully make this a much easier task.

http://macinchem.org/reviews/vortex/tut27/scripting_vortex27.php.

There are many more Hints, scripts and tutorials 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

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Substructure searching very large compound collections.

 

I described the use of the ability to script in Vortex multiple sub-structure searches using SMARTS. There are many occasions when this sort of feature is useful, if you want to flag molecules that contain reactive functional groups, toxicophores, or PAINS functional groups that have been shown to interfere with a variety of screens. Whilst the script worked fine it was rather slow for larger datasets, in the latest tutorial you can see how to take advantage of some of the latest features in Vortex to substantially improve search speeds allowing searching of 70 million compound collections on a desktop.

Scripting Vortex 24:- Substructure searching very large compound collections.

There are many more scripts listed on the Hints and Tutorials Page.

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Vortex scripts to access ChEMBL

 

ChEMBL is a manually curated chemical database of bioactive molecules . It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK. The database currently contains over 1.4 million unique structures with the associated activity at 10,579 different targets. It also acts as a repository for Open Access primary screening and medicinal chemistry data directed at neglected diseases.

Whilst the database can be downloaded, the data can also be accessed via a web interface (shown below) and a series of web services, these Vortex scripts show how it is possible to pull data from ChEMBL into Vortex.

As usual I’ve written it as a tutorial to try and offer some explanation how the script works, Scripting Vortex 23:- Accessing ChEMBL using Web Services

I think this rather nicely shows the power of web services and json.

There is a list of other Vortex scripts on the Hints and Tutorials page

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Scripting Vortex

 

One of the really neat features of the latest version of Vortex (> build 29622) is the ability to script multiple sub-structure searches using SMARTS. There are many occasions when this sort of feature is useful, if you want to flag molecules that contain reactive functional groups, toxicophores, or PAINS functional groups that have been shown to interfere with a variety of screens. Alternatively if you have a drug discovery project with multiple chemotypes you might want to tag particular groups of compounds as belonging to a named series to aid analysis.

The latest Vortex tutorial/script shows how to do this.


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Vortex script to classify acid, base, neutral

 

I’ve written several Vortex scripts that use external tools to calculate physicochemical properties including the use of ChemAxon (e.g. charge, pKa, logP, logD). However I often need to simply classify molecules as acid, base, neutral or zwitterion, so I’ve updated the script to create another column containing a text annotation.

vortex3

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Scripting Vortex 21, displayling web pages

 

Well things can change quickly at times, in the last tutorial I wrote..

Vortex has a limited capacity to render HTML, it is however a very limited ability so there is no support for javascript or CSS but you can introduce a number of useful extra features.

If you download the latest daily build of Vortex from the Dotmatics Support site there is a version that comes bundles with Java 8, if you download this version are a host of new options for displaying plots. In particular you can now display web pages, follow links on pages, and there is support for javascript.

In Scripting Vortex 21 there is a demonstration of this feature and an example script that uses SMARTCyp to predict sites of metabolism.

plotDemo3

There are many more scripts on the Hints and Tutorials Page.

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Scripting Vortex 20

 

Vortex has a limited capacity to render HTML, it is however a very limited ability so there is no support for javascript or CSS but you can introduce a number of useful extra features.

Im the latest tutorial you can find out how to use this to add images, plots and graphs to the molecular worksheet.

Scripting Vortex 20:-Adding images to Vortex

radarplots

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Scripting Vortex 19 Updated

 

This is another Vortex script, this one is used to implement a central nervous system penetration (CNS) algorithm described in the literature.

It is clear from many publications that a number of physicochemical properties influence central nervous system (CNS) penetration and it is often possible to play off one property against another in an effort to improve CNS penetration. An interesting paper from Wagner et al Moving beyond Rules: The Development of a Central Nervous System Multiparameter Optimization (CNS MPO) Approach To Enable Alignment of Druglike Properties describes an algorithm to score compounds with respect to CNS penetration.

The CNS MPO score was built based on six fundamental physicochemical properties: ClogP, ClogD, MW, TPSA, HBD, and pKa each weighted from 0 to 1.0

Update

One of the popular features in Vortex is to colour code columns, this is done automatically but sometimes you want to customise the colouring. For example in one set of values smaller values might be better, in another columns (perhaps an off-target activity) larger numbers might be better. Chatting to Sune Askjær, the author of the Unichem Script, it seemed that this might be a nice addition to this script.

The updated script is here.

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Scripting Vortex 19

 

This is another Vortex script, this one is used to implement a central nervous system penetration (CNS) algorithm described in the literature.

It is clear from many publications that a number of physicochemical properties influence central nervous system (CNS) penetration and it is often possible to play off one property against another in an effort to improve CNS penetration. An interesting paper from Wagner et al Moving beyond Rules: The Development of a Central Nervous System Multiparameter Optimization (CNS MPO) Approach To Enable Alignment of Druglike Properties describes an algorithm to score compounds with respect to CNS penetration.

The CNS MPO score was built based on six fundamental physicochemical properties: ClogP, ClogD, MW, TPSA, HBD, and pKa each weighted from 0 to 1.0 full details of the script are here.

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Un1Chem Vortex script updated.

 

The Vortex script that accesses Un1Chem has been updated. This is a minor bug fix.

Un1Chem is a new 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 databases. Currently the uniChem contains data from 21 different data sources:-



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Vortex runs on Raspberry Pi

 

A while back in a very neat demonstration of the portable coding approach Dotmatics released ElementalDB for the iPad an iPad application that does a substructure search of a 1,200,000 Chembl structure database in less than a second. Well now they have gone even further and ported their data visualisation tool Vortex to the raspberry Pi.

Raspberry Pi is a $35 credit-card sized computer that plugs into your TV and keyboard. It is used in electronics projects and for many of the functions usually assigned to a desktop PC such as spreadsheets, word-processing and games.  It features a 700MHz ARM processor and can run a Debian Linux derived operating system. Compiling Vortex on this platform took just a few minutes as it involved building upon Oracle’s JDK 7 which was recently released for the Pi.

pi

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Scripting Vortex to access Un1Chem

 

Un1Chem is a new 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 databases. Currently the uniChem contains data from 21 different data sources.

This script originally created by Sune Askjær first calculates the InChiKey for molecules in a workspace and then uses Un1Chem to search for information in multiple databases, then it provides a summary and a link to a locally generated summary table.

unichem2

Full details are here Scripting Vortex 18.

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Scripting Vortex 17 tutorial

 

In the tutorial Scripting Vortex 15 I showed how it is possible to create a contextual script for Vortex that downloaded a specific PDB file, then a FlexAlign Vortex script first identifies the structure column and then get the SMILES string of the selected molecule generates a 3D structure and uses Flex Align to do a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.

While this is useful if you have similar structures (perhaps analogues in a series) there will certainly be situations where it may be preferable to dock the new ligand into the binding site. The Scripting Vortex 17 tutorial describes how to achieve this.

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Scripting Vortex and MOE

One of the new features in the latest version of MOE from Chemical Computing Group is the Listener. The MOE socket listener provides an alternative to MOE/web for executing functions remotely on a running instance of MOE.

The script will download the associated PDB structures from the rcsb Protein Data Bank, put them into a database then start the browser. It may take a few seconds to download the structure; this does rely on MOE having the right proxy settings to access the internet (use the Java console to set them). You can now transfer this to MOE and amend the display to highlight the ligand.

The MOEflexalign script takes the SMILES string of the selected row generates a 3D structure and does a one-shot flexalign between the ligand in the system in MOE, and the incoming ligand.

It is probably easier to see this in action, if it appears rather small click on the YouTube icon in the bottom right corner of the video.

Full details are here




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Scripting Vortex 14

In tutorial 4 we looked at using the command line tool sddesc from Chemical Computing Group to calculate a number of molecular descriptors and then import them into Vortex. However there a couple of issues with doing this not the least ensuring all the environment variables are set correctly. An alternative is to use MOE as a web service and access the tools using the SOAP protocol (Simple Object Access Protocol). This protocol provides a specification for exchanging structured information in the implementation of Web Services in computer networks. It relies on XML Information Set for its message format.

Full details are here...



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Scripting Vortex, using OpenBabel fastsearch

One thing I’ve needed to do a couple of times recently is give an idea of how many similar compounds are available to the set of compounds I’m currently viewing. For example in designing a fragment library it is very useful to know for a particular fragment how many similar fragments are commercially available. Or when looking at the results of a high-throughput screen how many similar analogues to a particular hit were also screened.

To do this we need a way of doing a rapid similarity search of the reference database. I use OpenBabel in particular using the fast search capability with molecular fingerprints.

In Scripting Vortex 13 there is a new script to do this.

There are many more scripts and hints here.



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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



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Scripting Vortex:- Accessing a web service

I’ve just added the latest script for Vortex.

In previous scripts we have generated data using a local Java program, C program, PERL script, and SVL program. In this tutorial rather than have a local application generate the data we will use a web service.

mols

There are more scripts on the Hints and Tutorial pages.



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Scripting Vortex 10

I’ve just added a new tutorial on scripting Vortex, starting to add user interaction.

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Vortex script exchange

Vortex is an advanced data analysis package that understands chemistry, the capabilities of Vortex can be extended by the use of scripts. I’ve now created Vortex script exchange that users can use to download or share scripts.

There are also a series of scripting tutorials here to provide a starting point for creating new scripts.

Hopefully these scripts will be valuable to you.

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Scripting Vortex 9

I recently wrote a review of ForgeV10 in which I imported the results into Vortex for analysis. This works fine the only issue being the resulting structures are 3D which makes interpretation of the structure sometimes difficult to discern, this script uses OpenBabel to create SMILES which can be rendered as 2D images.

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Scripting Vortex 8 molecular shape matching

One of the critical activities of most drug discovery programs is the identification of novel leads, these hits can come from high throughput screening or fragment-based screening There is however great interest in virtual screening which allows the evaluation in silico of a vast number of compounds and the selection of a subset that have a greater chance of desired activity. The virtual screening can be achieved by searching using sub-structures or molecular descriptors, by docking potential ligands into the target protein and scoring the resulting docked pose, or by comparing with the shape and/or electrostatic map of a known ligand.

Shape-it is a tool developed by Silicos-it that aligns a reference molecule against a set of database molecules using the shape of the molecules as the align criterion. It is based on the use of Gaussian volumes as descriptor for molecular shape as it was introduced by Grant, J.A.; Gallardo, M.A.; Pickup, B.T. (1996) ‘A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape’,J. Comp. Chem. 17, 1653-1666.

This script shows how to run shape-it from within Vortex, bringing in the shape matching scores for filtering and analysis.

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Vortex script for MayaChemTools

I’ve just added a new Vortex script, this one uses a PERL script that is part of the excellent MayaChemTools.

Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using filter-it
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE
Scripting Vortex 5 Calculating similarities using OpenBabel
Scripting Vortex 6 Filtering compounds
Scripting Vortex 7 Using MayaChemTools

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Dotmatics LinkedIn Group

Thos who use LinkedIn might be interested to see that Dotmatics now have a dedicated group.

http://www.linkedin.com/groups/Dotmatics-4327915?

I wrote a review of the Dotmatics tools a while back and have written a series of scripts for Vortex.

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Scripting Vortex 6

I’ve just added another Vortex script. In this script we will make use of the ability of filter-it to categorise input molecules into 1) a set of molecules that fulfil all criteria as defined in the filter definition file (passed molecules), and 2) a set of molecules that do not fulfil at least one of the defined filter criteria (failed molecules). The filter file defines the criteria for acceptable calculated phisicochemical properties and also any substructures that should be included or excluded during the filtering. The filter file is a simple text file that users can define for themselves, there is a detailed explanation on the silicos-it website. They also provide several example filters “Leadlike”, “Druglike”, “CMCLike” and “Clean” which cleans up a file without imposing a “drug like” filter. It should be relatively straight-forward for users to create their own filters, one could imagine a rule-of-3 filter that might be used in fragment-based screening approaches, or a toxicphore filter based on SMARTS shown to be implicated in a specific toxicity. It might also be possible to define project specific filters if a project requires a specific profile. If you need help it might be worth contacting Silicos-it.

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Scripting Vortex 5

I’ve just posted the latest tutorial on scripting the chemically intelligent spreadsheet application Vortex, this tutorial shows how to use OpenBabel to provide similarity searching.

The full list of Vortex scripting tutorials are shown below.

Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using Sieve
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE
Scripting Vortex 5 Calculating similarities using OpenBabel

More hints and tutorials can be found here.

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Vortex developer wanted

This might be of interest.

Dotmatics is looking to expand the team working on Vortex, its data analysis platform. The candidate should have several years software development experience with Java and preferably with the Swing graphical user interface toolkit. The ideal candidate will have a degree or PhD in the life sciences, and will have experience with data visualisation and analysis techniques such as clustering. Experience with cheminformatics systems or statistical software, such as R, will be advantageous. Candidates will probably have experience working within the pharmaceutical/biotech sector or the life science software development industry.

The position will be based at the UK headquarters in Bishops Stortford (Herts, UK). We offer a competitive salary, benefits and a pleasant working environment at the Old Monastery site. Further information about the company and our software can be found at http://www.dotmatics.com.

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Scripting Vortex

This is the fourth tutorial on scripting Vortex a chemically intelligent data visualisation package. In the previous tutorials we have looked at getting data from OpenBabel, sieve, and cxcalc in this tutorial we will be using MOE as the compute engine. MOE from Chemical Computing Group is probably best known as a graphical user interface to a suite of computational chemistry tools, whilst this is indubitably the means by which many users will interact with the program it is worth finding out about the command-line tools that are available. These tools are often accessed by pipeline tools such as Knime to allow rapid processing of large files. CCG provides four very useful command-line tools in particular sddesc allows the calculation of some or all of the MOE molecular descriptors for each molecular entry.

The Vortex Scripts

Scripting Vortex Using OpenBabel
Scripting Vortex 2 Using Sieve
Scripting Votrex 3 Using cxcalc
Scripting Vortex 4 Using MOE

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Using Calculation Fields in Vortex

Whilst Vortex has tools that allow you to do some analysis and of course you can use the scripting facility to access statistical or model building packages like R in this tutorial we will be using a model taken from the literature and implementing it within Vortex using a calculation field to construct the algorithm.

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Scripting Vortex 3

ChemAxon's Calculator (cxcalc) is a really useful command line program in Marvin Beans and JChem that performs chemical calculations using calculator plugins. There are a lot of calculations provided by ChemAxon (e.g. charge, pKa, logP, logD), and others can be added by writing custom plugins, perhaps one of the most useful is the ability to calculate the acidic and basic pKa. Calculation of pKa is essential to get a reasonable hold on the LogD of a molecule. LogD is probably the most critical physicochemical property in drug discovery, it has a major influence on absorption, cell penetration, metabolism, CYP450 inhibition and induction, PGP transporter activity and activity at the HERG channel, and is often a critical component of any structure activity relationship.

These scripts make use of cxcalc to generate data columns in Vortex

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Scripting Vortex 2

This is the second page on scripting Vortex, on the first page I described how to use OpenBabel to calculate a limited selection of chemical properties. In this script we will use one of the brilliant tools from silicos.

SIEVE is a program for filtering out molecules with unwanted properties. It is based on the Open Babel open source C++ API for rapid calculation of 45 different molecular properties.

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Scripting Vortex

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