About WebChemistry

WebChemistry is a set of apps and services for chemical and biological computations, mostly focused on analysis of 3D structural patterns.

For questions regarding WebChemistry, please contact webchemistryhelpgmail.com.
David Sehnal
Development
Crina-Maria Ionescu, Lukáš Pravda
Feedback, testing, and documentation
Radka Svobodová Vařeková
Feedback and testing
PhD Thesis

PhD thesis dealing with the approaches used in the WebChemistry services can be found here.

PatternQuery

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.

MotiveValidator

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.

ValidatorDB

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.

MOLE

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.

Berka, K., Hanák, O., Sehnal, D., Banáš, P., Navrátilová, V., Jaiswal, D., Ionescu, C.M., Svobodová Vařeková, R., Koča, J., and Otyepka, M. (2012) MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels. Nucleic Acid Research, 40(W1): W222-W227.

Pravda, L., Berka, K., Svobodová Vařeková, R., Sehnal, D., Banáš, P., Laskowski, R., Koča, J. and Otyepka, M. (2014) Anatomy of enzyme channels. BMC bioinformatics, 15:379.

AtomicChargeCalculator

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.

SiteBinder

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.