Partial atomic charges for proteins

k 2021

Partial atomic charges for proteins

SCHINDLER, Ondřej, Tomáš RAČEK, Aleksandra MARŠAVELSKI, Radka SVOBODOVÁ, Jaroslav KOČA et. al.

Basic information

Original name

Partial atomic charges for proteins

Name (in English)

Partial atomic charges for proteins

Authors

SCHINDLER, Ondřej, Tomáš RAČEK, Aleksandra MARŠAVELSKI, Radka SVOBODOVÁ and Jaroslav KOČA

Edition

1st Student Conference in Structural Biology, 2021. 2021

Other information

Type of outcome

Prezentace na konferencích

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Změněno: 14/4/2022 08:03, RNDr. Ondřej Schindler, Ph.D.

Abstract

V originále

The distribution of the electron density determines many characteristics of the molecule. Electron density is difficult to represent; however, it can be approximated by the partial atomic charges, which are real numbers describing what portion of electron density belongs to each atom. These charges are often used in computational chemistry, chemo- and bioinformatics. Unfortunately, finding the electron density for large proteins is not possible. For this reason, faster but still reasonably accurate empirical methods must be used. These methods try to replicate the results of quantum mechanical (QM) calculations. Nevertheless, the calculation of partial atomic charges for proteins is not yet fully solved. Recently, we have developed the empirical method Split Charges Equilibration with Initial Parameterized Charges (SQE+qp) to tackle this issue. Additionally, we have suggested a new definition of the atomic types (i.e., grouping the atoms into the classes). In particular, each atom is assigned the type based on the elements of the bonded atoms. This fine-grained division ensures the precise assignment of the initial charges. However, such a model has many more parameters than the previous ones, so it was also necessary to design a faster parameterization technique [1]. To demonstrate our results, Figure 1 shows the strong correlation between the reference QM charges and charges of the parameterized SQE+qp model on the dataset of 60 proteins and 60 peptides. We currently work to extend this methodology to support the calculation of partial atomic charges for metalloproteins which we believe is the crucial step to calculate charges for the majority of proteins in the PDB database. The implementation of SQE+qp is included in Atomic Charge Calculator II [2], a web application available freely at https://acc2.ncbr.muni.cz.

Citovat

SCHINDLER, Ondřej, Tomáš RAČEK, Aleksandra MARŠAVELSKI, Radka SVOBODOVÁ and Jaroslav KOČA. Partial atomic charges for proteins. In 1st Student Conference in Structural Biology, 2021. 2021.

@proceedings{1847018,
   author = {Schindler, Ondřej and Raček, Tomáš and Maršavelski, Aleksandra and Svobodová, Radka and Koča, Jaroslav},
   booktitle = {1st Student Conference in Structural Biology, 2021.},
   title = {Partial atomic charges for proteins},
   url = {https://cssb.structbio.org/wp-content/uploads/1stSCSB_booklet_fin.pdf},
   year = {2021}
}

TY  - CONF
ID  - 1847018
AU  - Schindler, Ondřej - Raček, Tomáš - Maršavelski, Aleksandra - Svobodová, Radka - Koča, Jaroslav
PY  - 2021
TI  - Partial atomic charges for proteins
UR  - https://cssb.structbio.org/wp-content/uploads/1stSCSB_booklet_fin.pdf
N2  - The distribution of the electron density determines many characteristics of the molecule. Electron density is difficult to represent; however, it can be approximated by the partial atomic charges, which are real numbers describing what portion of electron density belongs to each atom. These charges are often used in computational chemistry, chemo- and bioinformatics. Unfortunately, finding the electron density for large proteins is not possible. For this reason, faster but still reasonably accurate empirical methods must be used. These methods try to replicate the results of quantum mechanical (QM) calculations. Nevertheless, the calculation of partial atomic charges for proteins is not yet fully solved. Recently, we have developed the empirical method Split Charges Equilibration with Initial Parameterized Charges (SQE+qp) to tackle this issue. Additionally, we have suggested a new definition of the atomic types (i.e., grouping the atoms into the classes). In particular, each atom is assigned the type based on the elements of the bonded atoms. This fine-grained division ensures the precise assignment of the initial charges. However, such a model has many more parameters than the previous ones, so it was also necessary to design a faster parameterization technique [1]. To demonstrate our results, Figure 1 shows the strong correlation between the reference QM charges and charges of the parameterized SQE+qp model on the dataset of 60 proteins and 60 peptides. We currently work to extend this methodology to support the calculation of partial atomic charges for metalloproteins which we believe is the crucial step to calculate charges for the majority of proteins in the PDB database. The implementation of SQE+qp is included in Atomic Charge Calculator II [2], a web application available freely at https://acc2.ncbr.muni.cz.
ER  -

SCHINDLER, Ondřej, Tomáš RAČEK, Aleksandra MARŠAVELSKI, Radka SVOBODOVÁ and Jaroslav KOČA. Partial atomic charges for proteins. In \textit{1st Student Conference in Structural Biology, 2021.}. 2021.

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