NEEMP: software for validation, accurate calculation and fast
parameterization of EEM charges

J 2016

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

RAČEK, Tomáš, Jana PAZÚRIKOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Aleš KŘENEK et. al.

Základní údaje

Originální název

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges

Autoři

RAČEK, Tomáš (203 Česká republika, domácí), Jana PAZÚRIKOVÁ (703 Slovensko, domácí), Radka SVOBODOVÁ VAŘEKOVÁ (203 Česká republika, domácí), Stanislav GEIDL (203 Česká republika, domácí), Aleš KŘENEK (203 Česká republika, domácí), Francesco Luca FALGINELLA (380 Itálie, domácí), Vladimír HORSKÝ (203 Česká republika, domácí), Václav HEJRET (203 Česká republika, domácí) a Jaroslav KOČA (203 Česká republika, garant, domácí)

Vydání

Journal of Cheminformatics, London, BIOMED CENTRAL LTD, 2016, 1758-2946

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10403 Physical chemistry

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.220

Kód RIV

RIV/00216224:14740/16:00091249

Organizační jednotka

Středoevropský technologický institut

DOI

http://dx.doi.org/10.1186/s13321-016-0171-1

UT WoS

000385466000002

Klíčová slova anglicky

Partial atomic charges; Electronegativity equalization method; EEM; EEM parameterization; wwPDB CCD database

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 22. 2. 2017 10:46, Mgr. Eva Špillingová

Anotace

V originále

Background The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equalization method (EEM) is the most frequently used approach for calculating partial atomic charges. EEM is fast and its accuracy is comparable to the quantum mechanical charge calculation method for which it was parameterized. Several EEM parameter sets for various types of molecules and QM charge calculation approaches have been published and new ones are still needed and produced. Methodologies for EEM parameterization have been described in a few articles, but a software tool for EEM parameterization and EEM parameter sets validation has not been available until now. Results We provide the software tool NEEMP (http://ncbr.muni.cz/NEEMP), which offers three main functionalities: EEM parameterization [via linear regression (LR) and differential evolution with local minimization (DE-MIN)]; EEM parameter set validation (i.e., validation of coverage and quality) and EEM charge calculation. NEEMP functionality is shown using a parameterization and a validation case study. The parameterization case study demonstrated that LR is an appropriate approach for smaller and homogeneous datasets and DE-MIN is a suitable solution for larger and heterogeneous datasets. The validation case study showed that EEM parameter set coverage and quality can still be problematic. Therefore, it makes sense to verify the coverage and quality of EEM parameter sets before their use, and NEEMP is an appropriate tool for such verification. Moreover, it seems from both case studies that new EEM parameterizations need to be performed and new EEM parameter sets obtained with high quality and coverage for key structural databases. Conclusion We provide the software tool NEEMP, which is to the best of our knowledge the only available software package that enables EEM parameterization and EEM parameter set validation. Additionally, its DE-MIN parameterization method is an innovative approach, developed by ourselves and first published in this work. In addition, we also prepared four high-quality EEM parameter sets tailored to ligand molecules.

Návaznosti

LM2015085, projekt VaV

Název: CERIT Scientific Cloud (Akronym: CERIT-SC)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CERIT Scientific Cloud

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

MUNI/A/0945/2015, interní kód MU

Název: Rozsáhlé výpočetní systémy: modely, aplikace a verifikace V.

Investor: Masarykova univerzita, Rozsáhlé výpočetní systémy: modely, aplikace a verifikace V., DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

RAČEK, Tomáš, Jana PAZÚRIKOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Aleš KŘENEK, Francesco Luca FALGINELLA, Vladimír HORSKÝ, Václav HEJRET a Jaroslav KOČA. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. Journal of Cheminformatics. London: BIOMED CENTRAL LTD, 2016, roč. 8, October, s. nestránkováno, 14 s. ISSN 1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-016-0171-1.

@article{1357233,
   author = {Raček, Tomáš and Pazúriková, Jana and Svobodová Vařeková, Radka and Geidl, Stanislav and Křenek, Aleš and Falginella, Francesco Luca and Horský, Vladimír and Hejret, Václav and Koča, Jaroslav},
   article_location = {London},
   article_number = {October},
   doi = {http://dx.doi.org/10.1186/s13321-016-0171-1},
   keywords = {Partial atomic charges; Electronegativity equalization method; EEM; EEM parameterization; wwPDB CCD database},
   language = {eng},
   issn = {1758-2946},
   journal = {Journal of Cheminformatics},
   title = {NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges},
   url = {http://jcheminf.springeropen.com/articles/10.1186/s13321-016-0171-1},
   volume = {8},
   year = {2016}
}

TY  - JOUR
ID  - 1357233
AU  - Raček, Tomáš - Pazúriková, Jana - Svobodová Vařeková, Radka - Geidl, Stanislav - Křenek, Aleš - Falginella, Francesco Luca - Horský, Vladimír - Hejret, Václav - Koča, Jaroslav
PY  - 2016
TI  - NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges
JF  - Journal of Cheminformatics
VL  - 8
IS  - October
SP  - nestránkováno
EP  - nestránkováno
PB  - BIOMED CENTRAL LTD
SN  - 17582946
KW  - Partial atomic charges
KW  - Electronegativity equalization method
KW  - EEM
KW  - EEM parameterization
KW  - wwPDB CCD database
UR  - http://jcheminf.springeropen.com/articles/10.1186/s13321-016-0171-1
L2  - http://jcheminf.springeropen.com/articles/10.1186/s13321-016-0171-1
N2  - Background The concept of partial atomic charges was first applied in physical and organic chemistry and was later also adopted in computational chemistry, bioinformatics and chemoinformatics. The electronegativity equalization method (EEM) is the most frequently used approach for calculating partial atomic charges. EEM is fast and its accuracy is comparable to the quantum mechanical charge calculation method for which it was parameterized. Several EEM parameter sets for various types of molecules and QM charge calculation approaches have been published and new ones are still needed and produced. Methodologies for EEM parameterization have been described in a few articles, but a software tool for EEM parameterization and EEM parameter sets validation has not been available until now. Results We provide the software tool NEEMP (http://ncbr.muni.cz/NEEMP), which offers three main functionalities: EEM parameterization [via linear regression (LR) and differential evolution with local minimization (DE-MIN)]; EEM parameter set validation (i.e., validation of coverage and quality) and EEM charge calculation. NEEMP functionality is shown using a parameterization and a validation case study. The parameterization case study demonstrated that LR is an appropriate approach for smaller and homogeneous datasets and DE-MIN is a suitable solution for larger and heterogeneous datasets. The validation case study showed that EEM parameter set coverage and quality can still be problematic. Therefore, it makes sense to verify the coverage and quality of EEM parameter sets before their use, and NEEMP is an appropriate tool for such verification. Moreover, it seems from both case studies that new EEM parameterizations need to be performed and new EEM parameter sets obtained with high quality and coverage for key structural databases. Conclusion We provide the software tool NEEMP, which is to the best of our knowledge the only available software package that enables EEM parameterization and EEM parameter set validation. Additionally, its DE-MIN parameterization method is an innovative approach, developed by ourselves and first published in this work. In addition, we also prepared four high-quality EEM parameter sets tailored to ligand molecules.
ER  -

RAČEK, Tomáš, Jana PAZÚRIKOVÁ, Radka SVOBODOVÁ VAŘEKOVÁ, Stanislav GEIDL, Aleš KŘENEK, Francesco Luca FALGINELLA, Vladimír HORSKÝ, Václav HEJRET a Jaroslav KOČA. NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. \textit{Journal of Cheminformatics}. London: BIOMED CENTRAL LTD, 2016, roč.~8, October, s.~nestránkováno, 14 s. ISSN~1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-016-0171-1.

Podrobný výpis o publikaci