So much to do, so little time

Trying to squeeze sense out of chemical data

Archive for the ‘benchmark’ 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

Datasets for Virtual Screening Benchmarks

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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 expected to non-toxic. Or combinations of these and other properties. Many methods are available for virtual screening including similarity, docking and predictive models.

So, given the plethora of methods which one do we use? There are many factors affecting choice of VS method including availability, price, computational cost and so on. But in the end, deciding which one is better than another depends on the use of benchmarks. There are two features of VS benchmarks: the metric employed to decide whether one method is better than another and the data used for benchmarking. This post focuses on the latter aspect.

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Written by Rajarshi Guha

October 9th, 2008 at 1:49 pm