(CTPIC)
v 1.1 (Spring 2020)
Process a structure file
Publication files:
CTPIC
The chemical composition of saccharide complexes underlies their biomedical activities as biomarkers for cardiometabolic disease, various types of cancer, and other conditions. However, because these molecules may undergo major structural modifications, distinguishing between compounds of saccharide and non-saccharide origin becomes a challenging computational problem that hinders the compilation of information about their bioactive moieties.We have developed an algorithm and software package called “Cheminformatics Tool for Probabilistic Identification of Carbohydrates” (CTPIC) that analyzes the covalent structure of a compound to yield a probabilistic measure for distinguishing saccharides and saccharide-derivatives from non-saccharides.
Results
CTPIC analysis of the RCSB Ligand Expo led to:- A substantial increase in the number of ligands characterized as saccharides. These compounds are listed under Publication files; Saccharide entries in Ligand Expo
- CTPIC analysis of Protein Data Bank identified 7.7% of the entries as saccharide-binding macromolecules.
These results are also available in JSON format through our page on the Open Science Framework.
CTPIC algorithm
- To try the algorithm you may use the Process a structure file link from the right-panel to upload a structure file, in MOL/SDF format.
- The Python source codes are availble through the CTPIC page on GitHub.
Citation:
- Hesam Dashti, William M. Westler, Jonathan R. Wedell, Olga V. Demler, Hamid R. Eghbalnia, John L. Markley & Samia Mora, Probabilistic identification of saccharide moieties in biomolecules and their protein complexes, Scientific Data volume 7, Article number: 210 (2020), https://doi.org/10.1038/s41597-020-0547-y, https://www.nature.com/articles/s41597-020-0547-y
Disclaimer:
- The custom source code, developed using Python3 in the Linux environment. This work is copyrighted under the terms of GPL, and the results are released under CC0 1.0 Universal of the Open Science Framework. The web-service and the source codes are provided on an “as is” basis without warranty of any kind, either expressed or implied. Any usage of the web-server, or modification and application of the source codes are free for academic use when CTPIC publications are cited.
- The NetwrokX library is used in the CTPIC source codes.
- The Open Babel software package is used in the CTPIC source codes.