Zobrazeno 1 - 10
of 112
pro vyhledávání: '"Jiří, Vondrášek"'
Autor:
Kateřina Faltejsková, Jiří Vondrášek
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-15 (2023)
Abstract Background The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger context of the bindin
Externí odkaz:
https://doaj.org/article/84f48c407cb349cb8415f3d26dec470b
Autor:
Jakub Galgonek, Jiří Vondrášek
Publikováno v:
Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-14 (2023)
Abstract Current biological and chemical research is increasingly dependent on the reusability of previously acquired data, which typically come from various sources. Consequently, there is a growing need for database systems and databases stored in
Externí odkaz:
https://doaj.org/article/564d8cb6e9214647a637fa5ef7ff9ff7
Autor:
Jakub Galgonek, Jiří Vondrášek
Publikováno v:
Journal of Cheminformatics, Vol 13, Iss 1, Pp 1-19 (2021)
Abstract The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF data and to explore links betwee
Externí odkaz:
https://doaj.org/article/ac472c91acdc45c19a1274e8e76ebf79
Autor:
Vyacheslav Tretyachenko, Jiří Vymětal, Tereza Neuwirthová, Jiří Vondrášek, Kosuke Fujishima, Klára Hlouchová
Publikováno v:
Open Biology, Vol 12, Iss 6 (2022)
The earliest proteins had to rely on amino acids available on early Earth before the biosynthetic pathways for more complex amino acids evolved. In extant proteins, a significant fraction of the ‘late’ amino acids (such as Arg, Lys, His, Cys, Trp
Externí odkaz:
https://doaj.org/article/ebcdbbd8b3e748d3bbb6f2d971278c54
Autor:
Adriano Rutz, Maria Sorokina, Jakub Galgonek, Daniel Mietchen, Egon Willighagen, Arnaud Gaudry, James G Graham, Ralf Stephan, Roderic Page, Jiří Vondrášek, Christoph Steinbeck, Guido F Pauli, Jean-Luc Wolfender, Jonathan Bisson, Pierre-Marie Allard
Publikováno v:
eLife, Vol 11 (2022)
Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and speci
Externí odkaz:
https://doaj.org/article/55a51ec0a5b9470e90e913bfceaefe5d
Autor:
Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger, Bengt Persson, Radka Svobodová Vařeková, Tomáš Raček, Jiří Vondrášek, Hedi Peterson, Ahto Salumets, Inge Jonassen, Rob Hooft, Tommi Nyrönen, Alfonso Valencia, Salvador Capella, Josep Gelpí, Federico Zambelli, Babis Savakis, Brane Leskošek, Kristoffer Rapacki, Christophe Blanchet, Rafael Jimenez, Arlindo Oliveira, Gert Vriend, Olivier Collin, Jacques van Helden, Peter Løngreen, Søren Brunak
Publikováno v:
Genome Biology, Vol 20, Iss 1, Pp 1-4 (2019)
Abstract Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalog
Externí odkaz:
https://doaj.org/article/c83588b2872a4b119b058a97f0ced0f7
Publikováno v:
Journal of Cheminformatics, Vol 11, Iss 1, Pp 1-7 (2019)
Abstract Motivation The existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields ranging from drug design to metabolomics. Transparent search across multiple databases
Externí odkaz:
https://doaj.org/article/f8bca1ae6607424491e11472c57ae50f
Publikováno v:
F1000Research, Vol 8 (2020)
EmbedSOM is a simple and fast dimensionality reduction algorithm, originally developed for its applications in single-cell cytometry data analysis. We present an updated version of EmbedSOM, viewed as an algorithm for landmark-directed embedding enri
Externí odkaz:
https://doaj.org/article/1939830147c34841b1d8e01ec2a8145b
Publikováno v:
Journal of Cheminformatics, Vol 10, Iss 1, Pp 1-11 (2018)
Abstract Background Structure search is one of the valuable capabilities of small-molecule databases. Fingerprint-based screening methods are usually employed to enhance the search performance by reducing the number of calls to the verification proce
Externí odkaz:
https://doaj.org/article/2c13d10fab504fe8a2109a2151431ae8
Publikováno v:
International Journal of Molecular Sciences, Vol 21, Iss 11, p 3986 (2020)
Interaction with the DNA minor groove is a significant contributor to specific sequence recognition in selected families of DNA-binding proteins. Based on a statistical analysis of 3D structures of protein–DNA complexes, we propose that distortion
Externí odkaz:
https://doaj.org/article/9a4b97a2aca7466c9a69a38ebec05280