Sometime back I was playing around with dynamic HTML and cam across a tutorial that described how to implement the dynamic suggestion feature that is commonly found on many websites (such as Google and Amazon). This set me wondering how I could use this mechanism to dynamically depict a SMILES string as I type it.
Archive for October, 2008
Depicting SMILES Dynamically
Posted in cheminformatics, software, tagged 2d, cdk, depiction, dynamic, html, smiles on October 28, 2008 | 2 Comments »
Surnames Across the Globe
Posted in visualization, tagged diaspora, indian, name on October 22, 2008 | 1 Comment »
I came across an interesting site called the World Names Profiler, which given a surname colors a map of the world based on frequency of occurence of the name in different countries. They have a dataset of 300 million names across 26 countries.
While it’s a nice visualization, it was very interesting for me to see [...]
Do the CDK Fingerprints Work?
Posted in cheminformatics, software, tagged benchmark, cdk, enrichment, fingerprint, pubchem, similarity on October 11, 2008 | 4 Comments »
In a previous post, I dicussed virtual screening benchmarks and some new public datasets for this purpose. I recently improved the performance of the CDK hashed fingerprints and the next question that arose is whether the CDK fingerprints are any good. With these new datasets, I decided to quantitatively measure how the CDK fingerprints compare [...]
Working With Fingerprints in R (can’t beat C!)
Posted in cheminformatics, software, tagged benchmark, c++, CRAN, fingerprint, R, similarity on October 11, 2008 | Leave a Comment »
Since I do a lot of cheminformatics work in R, I’ve created various functions and packages that make life easier for me as do my modeling and analysis. Most of them are for private consumption. However, I’ve released a few of them to CRAN since they seem to be generally useful.
One of them is the [...]
Datasets for Virtual Screening Benchmarks
Posted in cheminformatics, research, tagged benchmark, data, pubchem, virtual screening on October 9, 2008 | 1 Comment »
Virtual screening (VS) is a common task in the drug discovery process and is a computational method to identify promising compounds from a collection of hundreds to millions of possible compounds. What “promising” exactly means, depends on the context – it might be compounds that will likely exhibit certain pharmacological effects. Or compounds that are [...]
Which Bits are Important for Similarity Searches?
Posted in cheminformatics, research, tagged fingerprint, maccs, similarity, tanimoto on October 6, 2008 | Leave a Comment »
The recent paper by Wang and Bajorath is an interesting approach to identifying the important bits in a fingerprint, with respect to a dataset.
Their discussion focuses on the structural key type fingerprints (such as MACCS and the BCI fingerprints) and the problem they are trying to address is the fact that certain structural features may [...]
AJAX’ified Pub3D
Posted in cheminformatics, research, software, tagged cheminformatics, database, postgres, pubchem, ROCS, shape similarity, spatial on October 3, 2008 | Leave a Comment »
Pub3D is a 3D version of PubChem, in which we have generated a single conformer for 99% of PubChem using the smi23d suite of programs. The structures are then stored in a PostgreSQL database along with their distance moment shape descriptors described by Ballester and Graham-Richards. This allows us to perform shape similarity queries against [...]
