So much to do, so little time

Trying to squeeze sense out of chemical data

Archive for the ‘similarity’ tag

Working With Fingerprints in R (can’t beat C!)

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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 fingerprint package (version 2.9 was just uploaded to CRAN) , that is designed to read and manipulate fingerprint data generated from various cheminformatics toolkits or packages. Right now it supports output from the CDK, BCI and MOE. Fingerprints are represented using S4 classes. This allows me to override the R logical operators, so that one can do things like compute the logical OR of two fingerprints.

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Written by Rajarshi Guha

October 11th, 2008 at 12:14 am

Which Bits are Important for Similarity Searches?

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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 be more important for similarity searching than others. This is also related to the fact that molecular complexity (i.e., the number of structural features) can lead to bias in similarity calculations [1]. Given a dataset, an easy way to identify the important bits is the so called consensus approach [2, 3]- basically find out which bit positions are set to 1 for all (or a specified fraction) of the dataset. While useful, this can be misled if the target dataset has many molecules with a large number of structural features (so that many bits in the fingerprint will be set to 1).

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Written by Rajarshi Guha

October 6th, 2008 at 2:58 am