News
March 31, 2018
Probes & Drugs ver. 03.2018 was released!

We made it, and on the last day of March, we release the third version (03.2018) of the Probes and Drugs portal this year. 

Besides updated compound sets (SGC Probes, Guide to Pharmacology 2018.1 etc.), we added one brand new data set, the Kinase chemogenomic set, that was extracted from the paper Progress towards a public chemogenomic set for protein kinases and a call for contributions. Concretely, only compounds that meet the criteria for KCGS inclusion were added to the set.

This month, we've also started with the direct annotation of probe-target pairs, i.e., in case, that a probe has an assigned target/targets in the data extracted from its source, this target is now highlighted by a small probe icon next to its name (see the example below for the probe I-BRD9 and its target BRD9). So far, probes from Chemical probes.org, SGC Probes and Tool compound set are annotated, more sets will come in the near future.

We hope you’ll find the new data useful. If you have any suggestions for new functions or compound sets we could include to our database, please, let us know through the contact form.

Feb. 27, 2018
Probes & Drugs ver. 02.2018 is out!

Besides updated data sets and fixed bugs, there is one new ontology in this month's update, the ChEMBL's Gene Ontology slim was added to our current target ontologies. 

A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL

"The ‘ChEMBL protein target slim’ provides a means of firstly describing the biology of protein drug targets and secondly allows users to easily establish a connection between biological and chemical information regarding drugs and drug targets..."

You can access the ontology either from the Targets tab in the Compounds section or you can search for single terms from the ontology through our text search field.

We hope you’ll find the new data useful. If you have any suggestions for new functions or compound sets we could include to our database, please, let us know through the contact form.

Jan. 31, 2018
First version of Probes & Drugs in 2018 is out!

On the last day of January, Probe & Drugs ver. 01.2018 was released. In this version of our portal, there is one new compound set and two new filter types.

The one new compound set is the CeMM library of unique drugs (CLOUD) that 'covers prodrugs and active forms at pharmacologically relevant concentrations and is ideally suited for combinatorial studies' (A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor). Our set actually contains only the core 274 compounds (from the original 308 drugs, 34 STEAM drugs with unknown molecular target were excluded).

Concerning the new filter types, one of them is a Reference filter which is able to filter all compounds associated with a reference (i.e., publication, patent, etc.). This filter can be invoked by the filter icon next to a reference in the Targets & Pathways section of each compound, or through the search filed.

The second new filter type is so called special filter. We call it special because normally this type of filter is not available to be used in any database of bioactive compounds. There is currently only one special filter, Number of targets, but there are more to come. This filter is able to filter and sort compounds according to their promiscuity. It can be invoked through the search field or by the filter icon that appears when the mouse cursor is over the number of targets in the Targets & Pathways section. Using this filter, you can for example ask a question "How many approved drugs have more than 50 known targets?".

We hope you’ll find the new data and functionality useful. If you have any suggestions for new functions or compound sets we could include to our database, please, let us know through the contact form.

Dec. 21, 2017
Probes & Drugs ver. 12.2017 is out!

In the last update of Probes & Drugs this year, you can find two new data sets (besides the updated ones):

  1. DrugMatrix - "Comprehensive Rat Toxicogenomics Database and Analysis Tool"

  2. TargetMol - "Contains more than 3,470 small molecule compounds, pays more attention on their targets. All compounds have targets description, which is the key point to drug screening."

This month, we also extracted all references for our biactivity data from ChEMBL, Guide to pharmacology and BindingDB (DrugBank will come in a near future). Now, all these references can be easily accessed by clicking on the references icon in the header of a target in the Targets and pathways section of each compound.

We hope you’ll find the new data and functionality useful. If you have any suggestions for new functions or compound sets we could include to our database, please, let us know through the contact form.

Since the end of year is very near, we would also like to wish you a Merry Christmas, Happy New Year and lot of new Probes & Drugs in the year to come.

Nov. 29, 2017
Probes & Drugs ver. 11.2017 is out!

Probes & Drugs portal ver. 11.2017 is here with one brand new compound set and one new feature for the chemical space visualization.

The new compound set, Tool compound set, is a probe set published in Report and Application of a Tool Compound Data Set (J. Chem. Inf. Model.). This set consists mainly of compounds extracted from the ChEMBL database (based on stringent criteria for their potency, selectivity etc., for more details, see the paper) in combination with probes from the Chemical probes portal.

The new function of our chemical space visualization is the ability to use values associated with a filter (e.g., activities associated with a target filter) within the visualization. Anytime such filter is used, its values are automatically added as an attribute which can be accessed and used through the chemical space menu. As an example, in the picture below, you can see chemical space visualization based on the ligands of Androgen and Glucocorticoid receptor where the points are colored according to their activity on the Androgen receptor. The ones not associated with the filter are gray. 

Again, if you have any suggestions for new compound sets or new functions, or if you stumble on an error, please, let us know through the contact form.

Oct. 26, 2017
Probes & Drugs ver. 10.2017 is out!

For the Probes & Drugs portal ver. 10.2017, we prepared the integration of the BindingDB data and highly enriched the bioactivity data already found in our database. Apart from that, some of the compound sets underwent their monthly update together with the addition of the last two versions of the NIH Approved Oncology Drug set (ver. VII and VIII).

We hope you’ll find the new data useful and if you have any suggestions for new functions or if you stumble on an error, please, let us know through the contact form.

Sept. 28, 2017
Probes & Drugs ver. 09.2017 is out!

In this month's update you can find two new data sets (besides the updated ones):

  1. Drug Repurposing Hub - "Drug repurposing experiments are limited by the lack of comprehensive screening libraries. We introduce a best-in-class drug screening collection with more than 3,000 clinical drugs. The Repurposing Hub information resource contains extensive curated annotations for each drug, including details about commercial sources of all compounds. We invite you to explore the Hub information resource as a first step towards discovering new therapeutic applications for existing drugs."

  2. The Pathogen Box - "The Pathogen Box contains ~400 diverse, drug-like molecules active against neglected diseases of interest and is available free of charge."

We've also enriched our target information by incorporating the data (MOA) from DrugBank.

Finally, we've added one new function some of you asked us for: Custom set creation by matching to a supplied list/file of structures/names. So now, you can easily create custom sets by e.g., uploading your SDF file or by pasting of the list of names from an Excel file. You can try it here. The function is still in beta state, so don't hesitate to contact us in case you stumble on an error.

We hope you’ll find the new data and function useful. If you have any suggestions for new functions or compound sets we could include to our database, please, let us know through the contact form.

Aug. 26, 2017
Probes & Drugs ver. 08.2017 is out!

This month’s version is finally out with both updated and brand new data as well as new functions. If you are not here for the first time, you’ve probably noticed that we have updated our homepage and also set up the Probes & Drugs Twitter account (you can follow us here).

Besides updated data sets, we’ve added one new compound set, the Bioprocess diversity set, from a recent paper in Nature Chemical biology, Functional annotation of chemical libraries across diverse biological processes.

You can also use new functions that should help you to find and browse through the filters:

  1. You can list all filters by clicking on the List filters icon above the text search field. The filters are divided by their type and ordered by the number of compounds they represent.

  2. Since there can be really a lot of filters (hundreds, in some cases thousands) suggested by the autocomplete when using the text search field, you can now list the matched filters by pressing enter when no specific filter from the list is selected.

We hope you’ll find the new functions useful and if you have any suggestions for new functions or compound sets we could include to our database, please, let us know through the contact form.

July 28, 2017
Probes & Drugs portal in Nature Methods

We are excited to announce that the Probes & Drugs portal paper has just been published in the August issue of Nature Methods. Appart from the Correspondence itself, it also contains extensive Supplementary Notes with information about data processing, portal interface, data sources/tools and more. 

July 26, 2017
Probes & Drugs Portal official launch

As of the 26th July, the Probes and Drugs portal is officially released in order to be used by the research community. We hope it will give everoyne the opportunity to interactively explore the bioactive compound space in a way not achievable before. Have fun!