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Sub-pocket analysis method for Fragment-Based Drug Discovery

Kalliokoski, Tuomo, Olsson, Tjelvar and Vulpetti, Anna (2013) Sub-pocket analysis method for Fragment-Based Drug Discovery. Journal of Chemical Information and Modeling, 53 (1). pp. 131-141. ISSN 1549-9596


Although two binding sites might be overall dissimilar, they might still bind the same fragments if they share suitable sub-pockets. Information about shared sub-pockets can be used in fragment-based drug design to suggest new fragments or to replace existing fragments within an already known compound. A novel computational method called SubCav was developed which allows the similarity searching and alignment of sub-pockets from a PDB-wide database against a user-defined query. The method is based on pharmacophoric fingerprints combined with a sub-pocket alignment algorithm. SubCav was shown to be efficient in producing reasonable alignments for sub-pockets with low sequence similarity and be able to retrieve prospectively relevant sub-pockets from a large database even with different folds. It could also be used to analyze sub-pockets inside a protein family to facilitate drug design and selectivity rationalization.

Item Type: Article
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Additional Information: The publication also includes source code of the described method. The software is distributed under the BSD license license (, a standard and widely used open-source license.
Keywords: fragments, proteins, sub-pockets, similarity, fingerprints, alignment, fragment-based drug design
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Date Deposited: 13 Oct 2015 13:14
Last Modified: 13 Oct 2015 13:14


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