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@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 a 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, roč.~13, č.~1, s.~45-55. ISSN~1758-2946. Dostupné z: https://dx.doi.org/10.1186/s13321-021-00528-w.
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