Abstract
We present HiTSEE (High-Throughput Screening Exploration Environment), a visualization tool for the analysis of large chemical screens used to examine biochemical processes. The tool supports the investigation of structure-activity relationships (SAR analysis) and, through a flexible interaction mechanism, the navigation of large chemical spaces. Our approach is based on the projection of one or a few molecules of interest and the expansion around their neighborhood and allows for the exploration of large chemical libraries without the need to create an all encompassing overview of the whole library. We describe the requirements we collected during our collaboration with biologists and chemists, the design rationale behind the tool, and two case studies on different datasets. The described integration (HiTSEE KNIME) into the KNIME platform allows additional flexibility in adopting our approach to a wide range of different biochemical problems and enables other research groups to use HiTSEE.
Highlights
Genetics has been widely used in the past to study complex biological processes within a cellular system and to elucidate the function of proteins
Genetic approaches have proven to be extremely powerful in elucidating the principles of a wide range of biological processes, there are a number of substantial limitations to this approach, most importantly the lack of temporal control required to study dynamic processes, since a protein cannot be turned on or off on demand
Related work While there are a number of free and commercial tools that support one or more phases of high-throughput screening (HTS) (e.g., Spotfire), in the following we focus our review on visualization tools that address hit selection, exploration and expansion and the understanding of structure-activity relationships
Summary
Genetics has been widely used in the past to study complex biological processes within a cellular system and to elucidate the function of proteins. Genetic approaches have proven to be extremely powerful in elucidating the principles of a wide range of biological processes, there are a number of substantial limitations to this approach, most importantly the lack of temporal control required to study dynamic processes, since a protein cannot be turned on or off on demand. In order to switch a protein off, a compound needs to be identified that inhibits the protein under investigation and allows its function to be studied. For this purpose, high-throughput screening (HTS) is performed. This is a major technological breakthrough in biology experimentation [2]
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