Fast methods of atomic charge calculation: parameterization of
EEM for applicability to metal containing proteins

D 2010

Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Jakub VANĚK a Jaroslav KOČA

Základní údaje

Originální název

Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins

Název česky

Rychlé metody výpočtu atomových nábojů: Parametrizace EEM pro aplikaci na metaloproteiny

Autoři

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Jakub VANĚK a Jaroslav KOČA

Vydání

8th Discussions in Structural Molecular Biology, 2010

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10600 1.6 Biological sciences

Utajení

obsah je utajovanou skutečností

Odkazy

URL

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

partial charge, EEM, parameterization

Změněno: 20. 10. 2010 18:40, Mgr. Ing. Crina-Maria Ionescu, Ph.D.

Anotace

V originále

Atomic charges, although not physical observables, are used to explain many molecular properties and are needed in many molecular packages. The quantum chemical approach to calculating various types of atomic charges can be very precise, but extremely time demanding; in any case, its applicability to biomolecules is restricted by the size of the systems. One of the already available alternative solutions is the Electronegativity Equalization Method (EEM), which allows for the fast calculation of partial atomic charges with remarkable precision [1], provided that the proper parameters have been previously determined. Previous studies in this respect have made great progress since the original development of EEM by improving the formalism [2], increasing the number of covered atom types [3], testing the amenability of various atomic charge schemes [4], implementing the EEM formalism in modeling software [5] etc. However, none of them has dealt with system sizes of more than 200 atoms, a number which is hardly relevant at a biomolecular level. We have obtained EEM parameters for the elements commonly found in proteins (C, H, N, O, S) and the Ca ion that may appear as a ligand, for systems whose size is around 1000 atoms. All these systems are parts of very large proteins, and therefore the parameters we have obtained should be able to predict partial atomic charges on full-sized real proteins to a good approximation. We present the complete process of generating these EEM parameters.

Citovat

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Jakub VANĚK a Jaroslav KOČA. Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins. In 8th Discussions in Structural Molecular Biology. 2010.

@inproceedings{892318,
   author = {Ionescu, CrinaandMaria and Svobodová Vařeková, Radka and Vaněk, Jakub and Koča, Jaroslav},
   booktitle = {8th Discussions in Structural Molecular Biology},
   keywords = {partial charge, EEM, parameterization},
   language = {eng},
   title = {Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins},
   url = {http://www.xray.cz/setkani/abst2010/ionescu.htm},
   year = {2010}
}

TY  - JOUR
ID  - 892318
AU  - Ionescu, Crina-Maria - Svobodová Vařeková, Radka - Vaněk, Jakub - Koča, Jaroslav
PY  - 2010
TI  - Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins
KW  - partial charge, EEM, parameterization
UR  - http://www.xray.cz/setkani/abst2010/ionescu.htm
N2  - Atomic charges, although not physical observables, are used to explain many molecular properties and are needed in many molecular packages. The quantum chemical approach to calculating various types of atomic charges can be very precise, but extremely time demanding; in any case, its applicability to biomolecules is restricted by the size of the systems. One of the already available alternative solutions is the Electronegativity Equalization Method (EEM), which allows for the fast calculation of partial atomic charges with remarkable precision [1], provided that the proper parameters have been previously determined. Previous studies in this respect have made great progress since the original development of EEM by improving the formalism [2], increasing the number of covered atom types [3], testing the amenability of various atomic charge schemes [4], implementing the EEM formalism in modeling software [5] etc. However, none of them has dealt with system sizes of more than 200 atoms, a number which is hardly relevant at a biomolecular level. We have obtained EEM parameters for the elements commonly found in proteins (C, H, N, O, S) and the Ca ion that may appear as a ligand, for systems whose size is around 1000 atoms. All these systems are parts of very large proteins, and therefore the parameters we have obtained should be able to predict partial atomic charges on full-sized real proteins to a good approximation. We present the complete process of generating these EEM parameters.
ER  -

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Jakub VANĚK a Jaroslav KOČA. Fast methods of atomic charge calculation: parameterization of EEM for applicability to metal containing proteins. In \textit{8th Discussions in Structural Molecular Biology}. 2010.

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