The Protein Databank contains more than 110,000 macromolecular structures, a wealth of information for molecular life scientists. Application fields like drug design, red, green, and white biotechnology as well as fundamental research in structure-to-function relationships substantially profit from this data. With the increasing amount of structures, searching for information in this data becomes an important topic. While searching for text and sequences is an easy task, the situation looks completely different in case of structural queries.<br/> <br/>In this talk, we present a new database approach enabling structure-based searching in protein-ligand complexes. A flexible geometric query construction system allows the user to define geometric atom arrangements and combine them with textual elements to complex queries.  Highly efficient indexing techniques and different graph-based algorithms are used to rapidly detect all occurrences of the spatial query. Results can easily be analyzed and compared in a 3D viewer showing the structures aligned to the query. The database can also be used to browse molecular interaction geometries. In a special purpose application, the geometric arrangement of interacting atoms around functional groups can be searched, visualized and analyzed.<br/>These two sample applications demonstrate the abilities and usefulness of structural databases beyond flat file collections. They also show the need for novel  indexing techniques and algorithms to efficiently mine large sets of protein-ligand structures.<br/>

Geometric searching in large collections of protein-ligand interfaces

253rd National Meeting (2017)

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