Optimized SQE atomic charges for peptides accessible via a web application.

Area of Science:

• Computational Chemistry
• Chemoinformatics
• Bioinformatics
• Nanoscience

Background:

• Partial atomic charges are crucial in various scientific fields.
• Existing methods like EEM, QEq, and EQeq are fast but require empirical parameters and struggle with macromolecules.
• Split-charge Equilibration (SQE) and SQE+q0 show promise for peptides but lack accessible parameters and implementations.

Purpose of the Study:

• To develop a fast parameterization method for empirical charge calculation.
• To introduce an improved SQE method (SQE+qp) tailored for peptide datasets.
• To enhance accessibility of SQE methods through a web application.

Main Methods:

• Developed and compared an optimized guided minimization (optGM) method against the guided minimization (GDMIN) method.
• Introduced SQE+qp, an extension of SQE for peptide datasets.
• Integrated SQE and SQE+qp into the Atomic Charge Calculator II (ACC II) web application.

Main Results:

• optGM achieved fast parameterization, comparable to GDMIN but in significantly less time.
• SQE+qp demonstrated effectiveness for peptide datasets.
• SQE and SQE+qp methods, along with multiple parameter sets, are now available via ACC II and a command-line interface.

Conclusions:

• The ACC II web application and command-line tool provide accessible SQE methods and parameters.
• SQE+qp offers an excellent solution for charge calculations in peptide datasets.
• optGM facilitates efficient parameterization for methods with numerous parameters using large datasets.