Optimized SQE atomic charges for peptides accessible via a web
application

J 2021

Optimized SQE atomic charges for peptides accessible via a web application

SCHINDLER, Ondřej, Tomáš RAČEK, Aleksandra MARŠAVELSKI, Jaroslav KOČA, Karel BERKA et. al.

Basic information

Original name

Optimized SQE atomic charges for peptides accessible via a web application

Authors

SCHINDLER, Ondřej (203 Czech Republic, belonging to the institution), Tomáš RAČEK (203 Czech Republic, belonging to the institution), Aleksandra MARŠAVELSKI (191 Croatia), Jaroslav KOČA (203 Czech Republic), Karel BERKA (203 Czech Republic) and Radka SVOBODOVÁ (203 Czech Republic, guarantor, belonging to the institution)

Edition

Journal of Cheminformatics, Chemistry Central Ltd. in association with BioMed Central, 2021, 1758-2946

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 8.489

RIV identification code

RIV/00216224:14740/21:00121862

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1186/s13321-021-00528-w

UT WoS

000668532100001

Keywords in English

Partial atomic charges; Parameterization; Empirical methods; Web service

Abstract

V originále

Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity Equalization Method (EEM), Charge Equilibration method (QEq), and Extended QEq (EQeq). They all are fast, even for large molecules, but require empirical parameters. However, even these advanced methods have limitations—e.g., their application for peptides, proteins, and other macromolecules is problematic. An empirical charge calculation method that is promising for peptides and other macromolecular systems is the Split-charge Equilibration method (SQE) and its extension SQE+q0. Unfortunately, only one parameter set is available for these methods, and their implementation is not easily accessible.

Links

LM2018131, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

Citovat

SCHINDLER, Ondřej, Tomáš RAČEK, Aleksandra MARŠAVELSKI, Jaroslav KOČA, Karel BERKA and Radka SVOBODOVÁ. Optimized SQE atomic charges for peptides accessible via a web application. Journal of Cheminformatics. Chemistry Central Ltd. in association with BioMed Central, 2021, vol. 13, No 1, p. 45-55. ISSN 1758-2946. Available from: https://dx.doi.org/10.1186/s13321-021-00528-w.

@article{1779818,
   author = {Schindler, Ondřej and Raček, Tomáš and Maršavelski, Aleksandra and Koča, Jaroslav and Berka, Karel and Svobodová, Radka},
   article_number = {1},
   doi = {http://dx.doi.org/10.1186/s13321-021-00528-w},
   keywords = {Partial atomic charges; Parameterization; Empirical methods; Web service},
   language = {eng},
   issn = {1758-2946},
   journal = {Journal of Cheminformatics},
   title = {Optimized SQE atomic charges for peptides accessible via a web application},
   url = {https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00528-w},
   volume = {13},
   year = {2021}
}

TY  - JOUR
ID  - 1779818
AU  - Schindler, Ondřej - Raček, Tomáš - Maršavelski, Aleksandra - Koča, Jaroslav - Berka, Karel - Svobodová, Radka
PY  - 2021
TI  - Optimized SQE atomic charges for peptides accessible via a web application
JF  - Journal of Cheminformatics
VL  - 13
IS  - 1
SP  - 45
EP  - 45
PB  - Chemistry Central Ltd. in association with BioMed Central
SN  - 17582946
KW  - Partial atomic charges
KW  - Parameterization
KW  - Empirical methods
KW  - Web service
UR  - https://jcheminf.biomedcentral.com/articles/10.1186/s13321-021-00528-w
N2  - Partial atomic charges find many applications in computational chemistry, chemoinformatics, bioinformatics, and nanoscience. Currently, frequently used methods for charge calculation are the Electronegativity Equalization Method (EEM), Charge Equilibration method (QEq), and Extended QEq (EQeq). They all are fast, even for large molecules, but require empirical parameters. However, even these advanced methods have limitations—e.g., their application for peptides, proteins, and other macromolecules is problematic. An empirical charge calculation method that is promising for peptides and other macromolecular systems is the Split-charge Equilibration method (SQE) and its extension SQE+q0. Unfortunately, only one parameter set is available for these methods, and their implementation is not easily accessible.
ER  -

SCHINDLER, Ondřej, Tomáš RAČEK, Aleksandra MARŠAVELSKI, Jaroslav KOČA, Karel BERKA and Radka SVOBODOVÁ. Optimized SQE atomic charges for peptides accessible via a web application. \textit{Journal of Cheminformatics}. Chemistry Central Ltd. in association with BioMed Central, 2021, vol.~13, No~1, p.~45-55. ISSN~1758-2946. Available from: https://dx.doi.org/10.1186/s13321-021-00528-w.

Detailed Information on Publication Record