Document Detail


Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method.
MedLine Citation:
PMID:  23968236     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
We focused on the parameterization 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 parameterization 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 parameterized 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 0.097e, and average absolute error per atom 0.072e. The EEM models can be used with the freely available EEM implementation EEM_SOLVER.
Authors:
Crina-Maria Ionescu; Stanislav Geidl; Radka Svobodová Vařeková; Jaroslav Koca
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2013-8-22
Journal Detail:
Title:  Journal of chemical information and modeling     Volume:  -     ISSN:  1549-960X     ISO Abbreviation:  J Chem Inf Model     Publication Date:  2013 Aug 
Date Detail:
Created Date:  2013-8-23     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101230060     Medline TA:  J Chem Inf Model     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
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