Subscribe in a reader

Cambridge MedChem Consulting

ChEMBL 22 Released

ChEMBL 22 has been released. ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).

This version of the database, prepared on 8th August 2016 contains:

  • 2,043,051 compound records
  • 1,686,695 compounds (of which 1,678,393 have mol files)
  • 14,371,219 activities
  • 1,246,132 assays
  • 11,224 targets
  • 65,213 documents

There is more information in the ChEMBL blog post

Cheminformatics for Drug Design: Data, Models & Tools

Still a few places left at the Cheminformatics for Drug Design: Data, Models & Tools meeting organised by SCI's Fine Chemicals Group and RSC's Chemical Information and Computer Applications Group has been extended.

Imperial War Museum, Duxford, UK Wednesday 12 October 2016

Full details are available here https://www.soci.org/Events/Display-Event?EventCode=FCHEM481

Sounds an excellent meeting and you will have a chance to look around the aircraft at the Duxford Imperial War Museum.

Cheminformatics for Drug Design: Data, Models & Tools

I’ve just heard that the poster deadline for the Cheminformatics for Drug Design: Data, Models & Tools meeting organised by SCI's Fine Chemicals Group and RSC's Chemical Information and Computer Applications Group has been extended.

Imperial War Museum, Duxford, UK Wednesday 12 October 2016

Full details are available here https://www.soci.org/Events/Display-Event?EventCode=FCHEM481

Sounds an excellent meeting and you will have a chance to look around the aircraft at the Duxford Imperial War Museum.

Bringing Open Source to Drug Discovery demo

I spoke at the 25th Symposium on Medicinal Chemistry in Eastern England yesterday and gave a talk/demo on integrating Open Source software into Drug Discovery. I’ve now recorded the demo I showed and put it on YouTube

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

If you want any further information I’d be happy to try and help.

Bringing Open Source to Drug Discovery

I spoke at the 25th Symposium on Medicinal Chemistry in Eastern England yesterday and gave a talk/demo on integrating Open Source software into Drug Discovery. As I promised at the meeting I’ve published the slide deck that now includes 25 pages on links and resources that I hope you will find useful.

Bringing Open Source to Drug Discovery

If you want any further information I’d be happy to try and help.

A review of FAst MEtabolizer (FAME)

Whilst much computational work is undertaken to support, library design, virtual screening, hit selection and affinity optimisation the reality is that the most challenging issues to resolve in drug discovery often revolve around absorption, distribution, metabolism and excretion (ADME). Whilst we can measure the levels of parent drug in various medium tracking metabolic fate can often be a considerably more difficult proposition requiring significant resources. For this reason prediction of sites of metabolism has become the subject of current interest.

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). In addition dedicated models are available to predict sites of metabolism of phase I and II processes.

aspirinFame

FAME offers a high performance prediction of sites of metabolism mediated by a wide variety of mechanisms.

The full review is available here

SMARTCyp 2.4 released

The new SMARTCyp version 2.4 includes solvent accessible surface area (SASA) in the scoring function. SASA is computed using the 2DSASA algorithm from 2D coordinates.

smartcyp

  A paper describing the new models and their predictive accuracy on nine CYP isoforms is available in Molecular Pharmaceutics DOI

SMARTCyp Updated

SMARTCyp 2.3 has been released with some additional improvements including: Improved energies for N-oxidations Empirical correction for unlikely N-oxidations of tertiary alkylamines A filtering functionality for excluding compounds with very low activation barriers to CYP-mediated oxidations A smiles string can now be input directly on the command line using the -smiles flag.   Available as usual at http://www.farma.ku.dk/smartcyp   The science behind the improved N-oxidations and the empirical correction has also been published in a paper in Angewandte Chemie: DOI  

Viewing docking results in Vortex

This may be of interest.

I recently wrote a review of ForgeV10 from Cresset in which I actually imported the results into Vortex to do the analysis. There were however two issues with doing this, firstly interpretation of the 3D structures is sometimes difficult, this can be resolved by creating a 2D rendering of the structure. The other issue is trying to interpret the docking pose whilst looking at the analysis of the results in say a Vortex scatter plot.

I’ve been working with Mike Hartshorn and the people at Dotmatics who have incorporated OpenAstexViewer (a 3D molecule viewer) into the application you can read the full article here..

OSIRIS Property Explorer

I recently came across a website that may be of interest:

The OSIRIS Property Explorer shown in this page is an integral part of Actelion's (1) inhouse substance registration system. It lets you draw chemical structures and calculates on-the-fly various drug-relevant properties whenever a structure is valid. Prediction results are valued and color coded. Properties with high risks of undesired effects like mutagenicity or a poor intestinal absorption are shown in red. Whereas a green color indicates drug-conform behaviour.