Webchemistry is a set of tools and efficient data structures developed in C# by David Sehnal at co. at Masaryk University, Brno Czech Republic.
The toolkit employs and implements algorithms for comprehensive detection, analysis, and validation of 3D molecular patterns mainly comming from the Protein Data Bank and supports state of the art mmCIF format.
Run install-packages.bat or .ps1 in powershell (its enough to copy/paste it there - there is some silly default no script running policy).
To compile all projects:
- Visual Studio 2017 recommended.
- Silverlight 5 SDK (might be required to install the toolkit from silverlight.codeplex.com)
- IIS Express to debug the web.
Majority of these tools are available as webservices either in WebChemistry or MOLE Online.
Should you find this toolkit useful please cite one of the publications based on what you used:
- Sehnal, D., Pravda, L., Ionescu C.-M., Svobodová Vařeková, R. and Koča, J. (2015) PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res., 43, W383–W388.
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Svobodová Vařeková, R., Jaiswal, D., Sehnal, D., Ionescu, C.-M., Geidl, S., Pravda, L., Horský, V., Wimmerová, M. and Koča, J. (2014) MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res., 42, W227–33.
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Sehnal, D., Svobodová Vařeková, R., Pravda, L., Ionescu, C.-M., Geidl, S., Horský, V., Jaiswal, D., Wimmerová, M. and Koča, J. (2015) ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Res. 43, D369–D375.
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Sehnal, D., Vařeková, R.S., Berka, K., Pravda, L., Navrátilová, V., Banáš, P., Ionescu, C.M., Otyepka, M. and Koča, J. (2013) MOLE 2.0: Advanced approach for analysis of biomacromolecular channels. J. Cheminform., 5, 39.
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Ionescu,C.-M., Sehnal,D., Falginella,F.L., Pant,P., Pravda,L., Bouchal,T., Vařeková,R.S., Geidl,S. and and Koča,J. (2015) AtomicChargeCalculator: Interactive Web-based calculation of atomic charges in large biomolecular complexes and drug like molecules. J. Cheminform., 7, 50.
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Sehnal, D., Svobodová Vařeková, R., Huber, H. J., Geidl, S., Ionescu, C. M., Wimmerová, M. and Koča, J. (2012) SiteBinder: An improved approach for comparing multiple protein structural motifs. J. Chem. Inf. Model., 52(2), 343–359.