Atomic Charge Calculator II

Atomic Charge Calculator II (ACC II) is an application for fast calculation of partial atomic charges. It features 20 empirical methods along with parameters from literature. Short introduction covers the basic usage of ACC II. All methods and parameters are also available in a command-line application that can be used in user workflows.

Upload structure

Input file

Single sdf, mol2, pdb or mmcif file or archive (zip, tar.gz) of those files. Maximum file size: 10 MB

Examples

Dissociating hydrogens

This example focuses on acid dissociation of seven phenolic drugs, described in DrugBank. Their structures were obtained from PubChem. During the acid dissociation, these compounds release a hydrogen from the phenolic OH group. Using ACC II, we can examine a relation between pKa and a charge on the dissociating hydrogen. We found that the higher is pKa, the lower charge the hydrogen has (see table). This finding agrees with results published in literature.

Apoptotic protein activation

BAX protein regulates an apoptosis process. In our example, we show inactive BAX (PDB ID 1f16) and activated BAX (PDB ID 2k7w). The activation causes a charge redistribution that also includes C domain depolarization. This depolarization causes release of the C domain, which can then penetrate mitochondrial membrane and start the apoptosis as described in the literature.

Transmembrane protein

The nicotinic acetylcholine receptor passes the cell membrane (see the figure, part A) and serves as an ion channel (more details). We obtained its structure from Protein Data Bank Europe (PDB ID 2bg9), added missing hydrogens via WHAT IF and calculated the partial atomic charges using ACC II with default settings. Visualization of partial charges on the surface highlights the difference between nonpolar transmembrane part (mostly white due to charge around zero) and polar surface of extracellular and cytoplasmic parts (with mosaic of blue positive and red negative charges). The comparison demonstrates that this charge distribution agrees with receptor membrane position reported in literature.

If you found Atomic Charge Calculator II helpful, please cite: Raček, T., Schindler, O., Toušek, D., Horský, V., Berka, K., Koča, J., & Svobodová, R. (2020). Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Research. Are you interested in a research collaboration? Feel free to contact us.

Atomic Charge Calculator II is a part of services provided by ELIXIR – European research infrastructure for biological information.
For other services provided by ELIXIR's Czech Republic Node visit www.elixir-czech.cz/services .

Licence conditions in accordance with § 11 of Act No. 130/2002 Coll. The owner of the software is Masaryk University, a public university, ID: 00216224. Masaryk University allows other companies and individuals to use this software free of charge and without territorial restrictions in usual way, that does not depreciate its value. This permission is granted for the duration of property rights. This software is not subject to special information treatment according to Act No. 412/2005 Coll., as amended. In case that a person who will use the software under this licence offer violates the licence terms, the permission to use the software terminates.