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.
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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
Original language English
Type of outcome Article in a journal
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher Czech Republic
Confidentiality degree is not subject to a state or trade secret
WWW 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
Tags CF BioData, rivok
Tags International impact, Reviewed
Changed by Changed by: Mgr. Pavla Foltynová, Ph.D., učo 106624. Changed: 18/5/2022 13:10.
Abstract
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 projectName: 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
PrintDisplayed: 17/7/2024 05:30