Abstract
BackgroundPartial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites.Results This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular conformation and chemical environment. ACC relies on an empirical method to rapidly compute atomic charges with accuracy comparable to quantum mechanical approaches. Due to its efficient implementation, ACC can handle any type of molecular system, regardless of size and chemical complexity, from drug-like molecules to biomacromolecular complexes with hundreds of thousands of atoms. ACC writes out atomic charges into common molecular structure files, and offers interactive facilities for statistical analysis and comparison of the results, in both tabular and graphical form.ConclusionsDue to high customizability and speed, easy streamlining and the unified platform for calculation and analysis, ACC caters to all fields of life sciences, from drug design to nanocarriers. ACC is freely available via the Internet at http://ncbr.muni.cz/ACC.Electronic supplementary materialThe online version of this article (doi:10.1186/s13321-015-0099-x) contains supplementary material, which is available to authorized users.
Highlights
Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites
Implementation benchmark We have evaluated the accuracy and computational efficiency of the Electronegativity Equalization Method (EEM) Cutoff and EEM Cover approaches in a benchmark
The approaches are time efficient compared to Full EEM only when the molecule contains at least 10,000 atoms, but they are always more memory efficient
Summary
The ACC results are organized into hierarchical reports which are stored on the server for download or inspection for up to a month, at a unique URL visible only to the user. The overall report contains information and downloadable content (molecular structure files containing atomic charges, statistics of the results, information about all jobs) for all molecules. Pairwise comparison statistics between sets of charges resulted from different ACC jobs, or uploaded by the user. The 3D model can be built based on atomic positions, Fig. 3 Single molecule report provided by AtomicChargeCalculator It can be downloaded or inspected in the browser, and consists of several sections: summary information about the molecule, interactive list of values for all sets of charges, statistics within each set of charges, pairwise comparison statistics between sets of charges, and interactive 3D visualization of molecules and colored based on atomic charges, or built based on residue positions, and colored based on residue charges. A command line version of the application is available as an executable for users who wish to streamline more complex calculations
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
