Recent Posts
In memoriam Eric Dawson
It’s with great sadness that we note the passing our collaborator Eric Dawson. Through the BARD project we got to know Eric as a friendly, engaging and effective collaborator; his enthusiasms an... Read More
NCATSFind: Resolving Chemical Content in Browser
We have recently developed NCATSFind: a Firefox add-on to help users resolve web content to real chemical structures. The goal is to make discovering, displaying and downloading chemical structures as... Read More
Do structurally similar molecules have similar hash codes?
Molecular hash codes are fixed-length alphanumeric encoding of molecular graphs. They play a key role within chemical data management systems in facilitating (among other things) structural identity a... Read More
Hopping for success
Molecular scaffold is a fundamental concept in medicinal chemistry. Perhaps nowhere this is more apparent than during early stage discovery, where scaffolds are the primary means by which medicinal ch... Read More
PubChem fingerprint revisited
A few years ago we made available our implementation of the PubChem substructure keys fingerprint. Being it was our first attempt, there were a number of shortcomings with the implementation in terms ... Read More
An online version of the Lilly reactivity & promiscuity filters
Recently Bruns & Watson published a paper describing a set of rules to filter out (potenially) reactive and promiscuous small molecules. There are 275 rules addressing a variety of possible reason... Read More
Charting chemical space
Charting, in a technical sense, is the process of mapping objects in high dimensional space to lower dimensional subspace, something which we have previously discussed using the FastMap algorithm. In ... Read More
Library synthesizer
Update March 2, 2013: The complete code to this tool is available here. Library enumeration and profiling are an integral part of a medicinal chemist’s repertoire during early-stage discovery. W... Read More
Large scale substructure searching
Motivated by the recent renewed interest in substructure searching in the literature, we recently develop a proof-of-concept, self-contained substructure searching engine that can scale to large datab... Read More
MLBD browser
To date, the NIH Molecular Libraries Program (MLP)—through its comprehensive and specialized centers—has produced an unprecedented amount of experimental data characterizing various levels of inte... Read More
On faster substructure searching
With the rapid growth of chemical databases such as vendor catalogs and in-house screening collections, the constant desire to improve on (sub-) structure searching performance has never been more jus... Read More
The kinome navigator
In a recent paper, Metz et al. describe a statistical framework for constructing the kinome polypharmacology network. Using a large kinase panel (i.e., more than 150,000 activity values across 172 kin... Read More
The human kinome Java component
Update Feb. 2, 2013: This Java package is obsoleted; please checkout the latest code here. Recently, we received a request to be able to access to the human kinome dendrogram programmatically. We th... Read More
How many drugs are there?
Update May 29, 2011: Please see this post for the answer to the above question. The NCGC Pharmaceutical Collection (NPC), as we noted earlier, is a result of our ongoing efforts to construct a definit... Read More
The human kinome (part 1)
Update Nov 27, 2012: The entire source code for this tool is available here. Kinases are an important class of enzymes that are therapeutically relevant for a wide range of indications such as cancer ... Read More
Fragment activity profiler
A challenging task in early stage lead discovery is the triaging of chemical series from high throughput screening (HTS) assays. Here triaging is a multiplex problem that seeks to find the balance b... Read More