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A fast topological analysis algorithm for large-scale similarity evaluations of ligands and binding pockets.
- Source :
-
Journal of Cheminformatics . 12/1/2015, Vol. 7, p1-14. 14p. - Publication Year :
- 2015
-
Abstract
- Motivation: With the rapid increase of the structural data of biomolecular complexes, novel structural analysis methods have to be devised with high-throughput capacity to handle immense data input and to construct massive networks at the minimal computational cost. Moreover, novel methods should be capable of handling a broad range of molecular structural sizes and chemical natures, cognisant of the conformational and electrostatic bases of molecular recognition, and sufficiently accurate to enable contextually relevant biological inferences. Results: A novel molecular topology comparison method was developed and tested. The method was tested for both ligand and binding pocket similarity analyses and a PDB-wide ligand topological similarity map was computed. Conclusion: The unprecedentedly wide scope of ligand definition and large-scale topological similarity mapping can provide very robust tools, of performance unmatched by the present alignment-based methods. The method remarkably shows potential for application for scaffold hopping purposes. It also opens new frontiers in the areas of ligand-mediated protein connectivity, ligand-based molecular phylogeny, target fishing, and off-target predictions. [ABSTRACT FROM AUTHOR]
Details
- Language :
- English
- ISSN :
- 17582946
- Volume :
- 7
- Database :
- Academic Search Index
- Journal :
- Journal of Cheminformatics
- Publication Type :
- Academic Journal
- Accession number :
- 111358213
- Full Text :
- https://doi.org/10.1186/s13321-015-0091-5