Zobrazeno 1 - 10
of 23
pro vyhledávání: '"Jaroslav Koca"'
Publikováno v:
International Journal of Molecular Sciences, Vol 8, Iss 7, Pp 572-582 (2007)
The Electronegativity Equalization Method (EEM) is a fast approach for chargecalculation. A challenging part of the EEM is the parameterization, which is performedusing ab initio charges obtained for a set of molecules. The goal of our work was to pe
Externí odkaz:
https://doaj.org/article/bfd6d70de5504b3089ebbea794a96495
Autor:
Josef Houser, Stanislav Kozmon, Deepti Mishra, Zuzana Hammerova, Michaela Wimmerova, Jaroslav Koca
Publikováno v:
Acta Crystallographica Section A Foundations and Advances. 77:C689-C689
Autor:
Jaroslav Koča, Radka Svobodová Vařeková, Lukáš Pravda, Karel Berka, Stanislav Geidl, David Sehnal, Michal Otyepka
The book describes the individual steps necessary for biomacromolecular fragments analysis, as well as a list of essential software tools. For each step, it also shows corresponding web-based tools in detail and provides practical examples of their u
Publikováno v:
Nucleic Acids Research
One of the most interesting fields of mathematically oriented chemical research is the so-called computer-assisted organic synthesis design. These lecture notes elaborate the mathematical model of organic chemistry, which offers formal concepts for u
Autor:
Aliaksei Chareshneu, Purbaj Pant, Ravi José Tristão Ramos, David Sehnal, Tuğrul Gökbel, Crina-Maria Ionescu, Jaroslav Koča
Publikováno v:
ACS Omega, Vol 6, Iss 36, Pp 23023-23027 (2021)
Externí odkaz:
https://doaj.org/article/cc782d55f2904fca93544914bd086088
Autor:
Ondřej Schindler, Tomáš Raček, Aleksandra Maršavelski, Jaroslav Koča, Karel Berka, Radka Svobodová
Publikováno v:
Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-11 (2021)
Abstract Background 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 (
Externí odkaz:
https://doaj.org/article/169dbc18d0964272ae4286310036a6f8
Autor:
Adam Midlik, Veronika Navrátilová, Taraka Ramji Moturu, Jaroslav Koča, Radka Svobodová, Karel Berka
Publikováno v:
Scientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
Abstract Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Commun
Externí odkaz:
https://doaj.org/article/fa34aa4ea88b4f8c86eb1023bbd26b74
Publikováno v:
Journal of computational chemistry. 30(7)
The electronegativity equalization method (EEM) was developed by Mortier et al. as a semiempirical method based on the density-functional theory. After parameterization, in which EEM parameters A(i), B(i), and adjusting factor kappa are obtained, thi
Autor:
Navnit Kumar, Mishra, Petr, Kulhánek, Lenka, Snajdrová, Martin, Petrek, Anne, Imberty, Jaroslav, Koca
Publikováno v:
Proteins. 72(1)
We present the results of a series of 10-ns molecular dynamics simulations on Pseudomonas aeruginosa lectin-II (PA-IIL) and its complexes with four different monosaccharides. We compare the saccharide-free, saccharide-occupied, and saccharide- and io