Macs in Chemistry

Insanely Great Science

Implementing AB-MPS scoring

 

Whilst the rule of 5 (Ro5) has provided a useful way to describe small molecule drug space it is also clear that there are a significant number of molecular classes that exist beyond the rule of 5 boundaries (bRo5). In a review of the AbbVie compound collection DOI they were able to identify key findings that might explain the success (or failure) of bRo5 projects. From an analysis of a variety of calculated physicochemical properties they proposed a simple multiparametric scoring function (AB-MPS) was devised that correlated preclinical PK results with cLogD, number of rotatable bonds, and number of aromatic rings.

AB-MPS = Abs(cLogD-3) + NAR + NRB

Now implemented as a Vortex script.


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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


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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 ….


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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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