Some of the more popular pages on the site are the compilation of resources, a listing of Open-Source Cheminformatics toolkits and a list of useful python libraries for data science so I thought I'd flag a recent post by Pat Walters listing some interesting machine learning publications in 2020 on his practical cheminformatics blog.
His post AI in Drug Discovery 2020 is certainly an invaluable starting point.
infiniSee from BioSoveIT enables similarity searching, based on a query molecule, through billions of compounds in chemical spaces. Currently two chemical spaces from commercial compound vendors can be explored: the well-known Enamine REAL Space with 13 billion compounds and WuXi’s GalaXi with 1,7 billion compounds.
A recent publication described BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification DOI. There are a number of tools that predict sites of metabolism on a molecule and I've mentioned a couple FAME and SMARTCyp in the past. These packages flag potential metabolic hot spots (mainly for CYP mediated metabolism) but don't attempt to provide any information on the putative metabolites.
BioTransformer combines a machine learning approach with a knowledge-based approach to predict small molecule metabolism, and then calculate properties for the putative metabolites to aid metabolite ID
MNova NMR is Mestrelab Research’s NMR analysis program that can be used to quickly view, process and analyse both 1D and 2D spectra, as well as to easily produce publication quality assignments and images. The software can be downloaded from Mestrelab’s website (45-day free trial licences are available).
You can read the review here
The 2018.01 release of Chemical Computing Group's Molecular Operating Environment (MOE) software includes a number of new features, enhancements and changes. I written a review that highlights a number of the features.
ChemDraw is a very established chemical drawing package that probably set the standard for publication quality chemical drawing. However, on the Mac platform in particular I think it is true to say Cambridgesoft have taken their eye off the ball and released versions that were not up to their usual standard.
ChemDraw 17 is in someways a fresh beginning you can read the full review here.
FAME DOI is a collection of random forest models trained on a comprehensive and highly diverse data set of 20,000 small molecules annotated with their experimentally determined sites of metabolism taken from multiple species (rat, dog and human) designed to predict sites of metabolism. FAME 2 DOI builds on this work to improve accuracy ,in addition FAME 2 uses a slightly modified version of the visualization developed by Patrik Rydberg and implemented in SMARTCyp using ChemDoodle Web Components.
I've just written a review of the latest version of ChemDoodle3D
ChemDoodle 3D is a scientific visualization platform with a focus on user customizability and universal support. Just like its 2D counterpart, all of the graphics are fully customizable and controllable. The large feature set is well organized for intuitive access and we develop ChemDoodle 3D to work with the vast majority of graphics cards in use.
ChemDoodle3D really excels at the creation of high quality publication ready graphics, the ability to specifically select every atom or bond enables the user to precisely create the desired image. It performs well using modest hardware that would be accessible to any student. Perhaps one of the real attractions however is the ability to use the ChemDoodle Web Components to easily share structures via the web.
iScienceSearch is an internet search portal for scientists that allows you to perform a search across multiple data sources with a single query. I wrote a review a while back but it has undergone several updates since then and has been significantly expanded.
iScienceSearch allows both text and structure based searches, but the really interesting thing is that when you do a search using a single query item it automatically searchs in the background for other synonyms, structure, CAS Registry Number, InChI etc.
The screenshot below (click to enlarge) was generated using a structure-based query, as you can see the search results also include the results from text-based queries using synonyms. The filters on the left-hand side allow you to sort and filter the results to allow you to focus on the most relevant information.
The searching is free and requires no registration.
The Medicinal Chemistry Toolkit is one of the best examples yet to show how mobile devices are making an impact in science. It is becoming the "swiss army knife" for medicinal chemists with an increasing calculators that are critical for drug design. To be honest I think a lot of biologists will find it useful as well.
When I first started the list of data analysis packages for Mac OS X it was a fairly short list, over the years the list has grown and the diversity of packages increased. From free packages like R to enterprise applications like IBM SPSS costing thousands. Some packages are enormously powerful but have a ferocious learning curve, whilst others are very easy to use but have only very limited capabilities. Wizard is an intuitive data analysis tool, designed from the ground up to be readily accessible but still retain the power of the sophisticated command line driven applications that only seem suitable for programmers. Wizard Pro allows the user to explore the data interactively without the need to learn a programming language. Read more here.
I should have added Wizard Pro runs under Yosemite and is on the list of Yosemite compatible applications, and has just been updated to version 1.6.7 (Feb 27th).
This is an update to a blog post from early 2013 incorporating some valuable readers comments.
For many years I’ve used the excellent Clipboardsharing to exchange the clipboard contents between my laptop and desktop machines, it also supports multiple clipboards. However it is not supported under Mac OS X 10.7.x (Lion) and the developer website seems to have disappeared. I spent a while looking at various alternatives and I thought I’d summarise my findings.
I’ve just written a review of Stardrop an application from Optibrium that was designed to aid decision making for scientists involved in drug discovery that has recently been updated.
- Virtual Library Enumeration – The Nova plug-in module for StarDrop now has the added ability to quickly and easily enumerate a virtual library based on a template scaffold that you define with substitution points and variable fragments. You can sketch the groups to substitute at each point, select them from a user-defined or centrally administered library, or take them from a decomposition of another series using the R-group analysis tool in StarDrop
- Data visualisation - now allows you to apply interactive filters to your graphs and plots to quickly focus on the most interesting compounds. StarDrop now also supports the analysis of dates allowing you to explore variations of properties or scores with time
- Clustering - this new tool enables you to easily identify groups of similar compounds within a data set, based on either their structural similarity or properties
- Dataset Filtering - this helps you to remove compounds from a data set with unwanted sub-structures or property values. You can define any number of criteria with which to filter a data set
- Duplicate Removal - when combining compound data from multiple sources it’s common to end up with multiple copies of the same compound in a single data set. The duplicate removal tool makes it easy to find these and choose the entries that you want to keep.
- ADME QSAR – new model for predicting log([Brain]:[Blood]) (the old model remains available for consistency with previously calculated results)
- StarDrop now includes a FieldAlign module, using Cresset's molecular Field technology, provides a unique, 3-dimensional (3D) insight into the biological activity, properties and interactions of your compounds.
There is a comprehensive list of software reviews here.