Partial atomic charges for proteins

SCHINDLER, Ondřej, Tomáš RAČEK, Radka SVOBODOVÁ VAŘEKOVÁ and Jaroslav KOČA. Partial atomic charges for proteins. In ELIXIR CZ Annual Conference 2019. 2019. ISBN 978-80-86241-61-6.

Basic information

• Original name: Partial atomic charges for proteins
• Authors: SCHINDLER, Ondřej (203 Czech Republic, belonging to the institution), Tomáš RAČEK (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, guarantor, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, belonging to the institution).
• Edition: ELIXIR CZ Annual Conference 2019, 2019.

Other information

• Original language: English
• Type of outcome: Conference abstract
• 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
• RIV identification code: RIV/00216224:14740/19:00111277
• Organization unit: Central European Institute of Technology
• ISBN: 978-80-86241-61-6
• Keywords in English: Partial atomic charges; proteins
• Tags: rivok

Abstract

The concept of partial atomic charges proved as very useful in many fields of chemistry. In general, partial atomic charges are an approximation of electron densities in orbitals to real numbers related to atoms. However, since using the quantum chemistry method for calculation of partial charges is computationally demanding, a large number of empirical methods have been developed to speed-up the calculation. These empirical methods were successfully calibrated (parameterized) for small molecules. Their usage for proteins is still challenging. In my contribution, I discuss an applicability of selected empirical methods (including a novel approach ACKS2) in combination with several atomic types definition for calculation of charges in proteins.

Links

• LQ1601, research and development project: Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR