Fingerprint Similarity Searches in MongoDB

A few of my recent projects have involved the use of MongoDB, primarily for the ease afforded by a schemaless environment. Sometime back I had investigated the use of MongoDB to store chemical structure data, though those efforts did not actually query structures per se; instead they queried for precomputed numeric or text properties. So […]

High Content Screens and Multivariate Z’

While contributing to a book chapter on high content screening I came across the problem of characterizing screen quality. In a traditional assay development scenario the Z factor (or Z’) is used as one of the measures of assay performance (using the positive and negative control samples). The definition of Z’ is based on a […]

Cheminformatics and Non-Relational Datastores

Over the past year or so I’ve been seeing a variety of non-relational data stores coming up. They also go by terms such as document databases or key/value stores (or even NoSQL databases). These systems are alternatives to traditional RDBMS’s in that they do not require explicit schema defined a priori. While they do not […]

Performance of AtomContainerSet versus ArrayList

In my previous post, I had asked whether we really need AtomContainerSet and other related specialized container classes as opposed to using parametrized List objects. Gilleain had mentioned some issues that might require these specialized classes. But at this point it’s not clear to me what the intended goal for these classes was. For now, […]

Quick Comments on an Analysis of Antithrombotics

Joerg has made a nice blog post on the use of Open Source software and data to analyse the occurence of antithrombotics. More specifically he was trying to answer the question Which XRay ligands are closest to the Fontaine et al. structure-activity relationship data for allowing structure-based drug design? Using Blue Obelisk tools and ChemSpider […]