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.
- IIS Express to debug the web.
- (Optional) 7-zip for helper service deployment scripts.
Use msbuild /t:Restore to install the deps.
To deploy the web, use Publish option for the Webchemistry.Web project in Visual Studio. Use Default Web Site\Platform as AppPath.
To update services, use the commands in DeployHelper directory. After copying the new binaries to the WebChemUtils directory at E:, run the Bootstrapper to update the versions of the services.
Majority of these tools are available as webservices either in WebChemistry or MOLEonline.
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.