title: Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method.
abstract: We focused on the parametrization and evaluation of empirical models for fast and accurate calculation of conformationally dependent atomic charges in proteins. The models were based on the electronegativity equalization method (EEM), and the parametrization procedure was tailored to proteins. We used large protein fragments as reference structures and fitted the EEM model parameters using atomic charges computed by three population analyses (Mulliken, Natural, iterative Hirshfeld), at the Hartree-Fock level with two basis sets (6-31G*, 6-31G**) and in two environments (gas phase, implicit solvation). We parametrized and successfully validated 24 EEM models. When tested on insulin and ubiquitin, all models reproduced quantum mechanics level charges well and were consistent with respect to population analysis and basis set. Specifically, the models showed on average a correlation of 0.961, RMSD 0.097 e, and average absolute error per atom 0.072 e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.
authors: CEITEC-Central European Institute of Technology, and National Centre for Biomolecular Research, Faculty of Science, Masaryk University Brno , Kamenice 5, 625 00, Brno-Bohunice, Czech Republic.
authors: Crina-Maria
authors: CM
authors: Ionescu
authors: Stanislav
authors: S
authors: Geidl
authors: Radka
authors: R
authors: Svobodová Vařeková
authors: Jaroslav
authors: J
authors: Koča
mesh_terms: D003198:Computer Simulation; D030562:Databases, Protein; D005740:Gases; D006801:Humans; D007328:Insulin / Q000737:chemistry*; D008956:Models, Chemical; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D012680:Sensitivity and Specificity; D012984:Software; D012996:Solutions; D055672:Static Electricity; D013997:Time Factors; D025801:Ubiquitin / Q000737:chemistry*
chemical_list: D005740:Gases; D007328:Insulin; D010446:Peptide Fragments; D012996:Solutions; D025801:Ubiquitin