Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method

2013 ◽  
Vol 53 (10) ◽  
pp. 2548-2558 ◽  
Author(s):  
Crina-Maria Ionescu ◽  
Stanislav Geidl ◽  
Radka Svobodová Vařeková ◽  
Jaroslav Koča
Keyword(s):  
Atomic Charges ◽  
Electronegativity Equalization ◽  
Electronegativity Equalization Method ◽  
Rapid Calculation ◽  
Equalization Method

Electronegativity-equalization method for the calculation of atomic charges in molecules

1986 ◽  
Vol 108 (15) ◽  
pp. 4315-4320 ◽  
Author(s):  
Wilfried J. Mortier ◽  
Swapan K. Ghosh ◽  
S. Shankar
Keyword(s):  
Atomic Charges ◽  
Electronegativity Equalization ◽  
Electronegativity Equalization Method ◽  
Equalization Method

Reactions and Segregation on α-Cristobalite (011) Surfaces by the Electronegativity Equalization Method

1992 ◽  
Vol 291 ◽  
Author(s):  
W. M. Mullins
Keyword(s):  
Surface Charge ◽  
Driving Force ◽  
Atomic Charges ◽  
Electronegativity Equalization ◽  
Electronegativity Equalization Method ◽  
Electronegativity Difference ◽  
Surface Hydration ◽  
Framework Energy ◽  
Effect Of Surface ◽  
Equalization Method

ABSTRACTThe electronegativity equalization method is used to calculate the atomic charges, framework electronegativity and framework energy of the α–cristobalite bulk and the relaxed (011) surface. The effect of surface hydration and fluoridation on the framework properties are then calculated and related to surface charge. The segregation of germanium, aluminum and phosphorus in the α-cristobalite structure are modelled using the same method. The framework electronegativity difference between surface and bulk is observed to be a driving force for reactions and segregation.

scholarly journals Electronegativity Equalization Method: Parameterization and Validation for Large Sets of Organic, Organohalogene and Organometal Molecule

2007 ◽  
Vol 8 (7) ◽  
pp. 572-582 ◽  
Author(s):  
Radka Varekova ◽  
Zuzanna Jirouskova ◽  
Jakub Vanek ◽  
Simon Suchomel ◽  
Jaroslav Koca
Keyword(s):  
Electronegativity Equalization ◽  
Large Sets ◽  
Electronegativity Equalization Method ◽  
Equalization Method

STUDY ON COMPLEXES OF TRYPSIN AND ITS INHIBITORS BY MEANS OF ATOM-BOND ELECTRONEGATIVITY EQUALIZATION METHOD FUSED INTO MOLECULAR MECHANICS (ABEEM/MM)

2007 ◽  
Vol 06 (04) ◽  
pp. 731-746 ◽  
Author(s):  
QING-MEI GUAN ◽  
ZHONG-ZHI YANG
Keyword(s):  
Hydrogen Bond ◽  
Bond Length ◽  
Molecular Mechanics ◽  
Trypsin Inhibitor ◽  
Electrostatic Interactions ◽  
Hydrogen Atoms ◽  
Electronegativity Equalization ◽  
Electronegativity Equalization Method ◽  
Atom Bond ◽  
Equalization Method

Trypsin is one of the most important enzymes and plays important roles in the regulation of biological processes. The newly developed trypsin–inhibitor interaction potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) was employed to study complexes of trypsin and its inhibitors. Some structural properties, including root-mean-square deviations (RMSD) of bond length, bond angle and key dihedral, and coordinated RMS Shifts of atoms and hydrogen bond, were studied using ABEEM/MM method and compared with OPLS-AA force-field. At the same time, comparative study on the charges of the hydrogen atoms at the tail of the ligand was also discussed in order to investigate the effect of hydrogen bond between trypsin and its ligand. This work demonstrates that ABEEM/MM model can well reproduce good structures for these trypsin–inhibitor complexes with rather small RMSD of bond length, bond angles, key dihedrals, and RMS Shifts of atomic coordinates with respect to the experimental crystal structures, compared with the results from the OPLS-AA method. The charges obtained by ABEEM/MM model are in good accordance with those from an ab initio calculation. Moreover, both the polarization and the salt-bridge effects have been taken into account. It is shown that ABEEM charges can properly describe the electrostatic interactions between the protein trypsin and its inhibitors.

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