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

D 2010

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

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš RADĚJ, Ondřej SKŘEHOTA, Jaroslav KOČA et. al.

Základní údaje

Originální název

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

Název česky

Rychlé metody výpočtů nábojů: parametrizace EEM pro uplatnění na proteiny

Autoři

IONESCU, Crina-Maria, Radka SVOBODOVÁ VAŘEKOVÁ, Tomáš RADĚJ, Ondřej SKŘEHOTA a Jaroslav KOČA

Vydání

8th European Conference on Computational Chemistry, 2010

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10600 1.6 Biological sciences

Utajení

není předmětem státního či obchodního tajemství

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

atomic charge; EEM; parameterization

Příznaky

Mezinárodní význam

Změněno: 20. 10. 2010 15:49, Mgr. Ing. Crina-Maria Ionescu, Ph.D.

Anotace

V originále

Atomic charges, although not physical observables, are called upon to explain many molecular properties and are used by many computational chemistry software 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 modelling software [5] etc. However, none of them has dealt with system sizes of more than 200 atoms, a number which is hardly relevant at the 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, Tomáš RADĚJ, Ondřej SKŘEHOTA a Jaroslav KOČA. Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins. In 8th European Conference on Computational Chemistry. 2010.

@inproceedings{898029,
   author = {Ionescu, CrinaandMaria and Svobodová Vařeková, Radka and Raděj, Tomáš and Skřehota, Ondřej and Koča, Jaroslav},
   booktitle = {8th European Conference on Computational Chemistry},
   keywords = {atomic charge; EEM; parameterization},
   language = {eng},
   title = {Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins},
   year = {2010}
}

TY  - JOUR
ID  - 898029
AU  - Ionescu, Crina-Maria - Svobodová Vařeková, Radka - Raděj, Tomáš - Skřehota, Ondřej - Koča, Jaroslav
PY  - 2010
TI  - Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins
KW  - atomic charge
KW  - EEM
KW  - parameterization
N2  - Atomic charges, although not physical observables, are called upon to explain many molecular properties and are used by many computational chemistry software 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 modelling software [5] etc. However, none of them has dealt with system sizes of more than 200 atoms, a number which is hardly relevant at the 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, Tomáš RADĚJ, Ondřej SKŘEHOTA a Jaroslav KOČA. Fast methods of atomic charge calculation: parameterization of EEM for applicability to proteins. In \textit{8th European Conference on Computational Chemistry}. 2010.

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