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A central problem in structure-based drug design is understanding protein–ligand interactions quantitatively and qualitatively. Several recent studies have highlighted from a qualitative perspective the nature of these interactions and their utility in drug discovery. However, a common limitation is a lack of adequate tools to mine these interactions comprehensively, since exhaustive searches of the protein data bank are time-consuming and difficult to perform. Consequently, fundamental questions remain unanswered: How unique or how common are the protein–ligand interactions observed in a given drug design project when compared to all complexed structures in the protein data bank? Which interaction patterns might explain the affinity of a tool compound toward unwanted targets? To answer these questions and to enable the systematic and comprehensive study of protein–ligand interactions, we introduce PROLIX (Protein Ligand Interaction Explorer), a tool that uses sophisticated fingerprint representations of ...
| Authors: | Martin Weisel; Hans-Marcus Bitter; François Diederich; W. Venus So; Rama Kondru | |
| Journal: | Journal of Chemical Information and Modeling | |
| Year: | 2012 | |
| DOI: | 10.1021/ci300034x | |
| Publication date: | 01-06-2012 |
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