Abstract
We have generated a number of compound data sets and programs for different types of applications in pharmaceutical research. These data sets and programs were originally designed for our research projects and are made publicly available. Without consulting original literature sources, it is difficult to understand specific features of data sets and software tools, basic ideas underlying their design, and applicability domains. Currently, 30 different entries are available for download from our website. In this data article, we provide an overview of the data and tools we make available and designate the areas of research for which they should be useful. For selected data sets and methods/programs, detailed descriptions are given. This article should help interested readers to select data and tools for specific computational investigations.
Highlights
For compound data mining and the development and evaluation of chemoinformatics methods, public domain databases have become indispensable resources
Some of the older activity classes that are still available from our website have originated from the license-restricted Molecular Drug Data Report (MDDR)7
20 activity classes (ACs) assembled from the literature and 15 ACs collected from MDDR Eight ACs
Summary
For compound data mining and the development and evaluation of chemoinformatics methods, public domain databases have become indispensable resources. Major public repositories include PubChem, BindingDB2, ChEMBL3, and ZINC4. While the former three databases contain compounds and bioactivity data, the latter collects commercially available compounds that are typically not annotated with activity information. Bioactivity data are usually obtained from original literature or patent sources. From these databases, screening data sets (PubChem) and compound activity classes (BindingDB, ChEMBL) can be extracted. Benchmarking of newly developed computational methods typically depends on the availability of such activity classes.
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