Biofizicnij Visnik最新文献

{"title":"Svante Pääbo's paleogenomics results in the context of post-academic transformations of modern technoscience (strokes to the portrait of the Nobel laureate in the socio-cultural context)","authors":"V. F. Cheshko","doi":"10.26565/2075-3810-2022-48-03","DOIUrl":"https://doi.org/10.26565/2075-3810-2022-48-03","url":null,"abstract":"The studies of Svante Pääbo, Nobel Laureate in Physiology or Medicine in 2022 are analyzed in two aspects: firstly, as the most striking example of the evolutionary transformation of classical science into the so-called post-academic (techno)science and, secondly, as an element of the so-called \"biopolitical turn\" in the socio-humanitarian and political knowledge of technological civilization and, in particular, in the concept of \"civil society\".","PeriodicalId":31658,"journal":{"name":"Biofizicnij Visnik","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135440948","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ProtNA-ASA data base: new version including information about electrostatic potential of DNA minor groove","authors":"M. Yu. Zhytnikova, A. V. Shestopalova","doi":"10.26565/2075-3810-2022-48-02","DOIUrl":"https://doi.org/10.26565/2075-3810-2022-48-02","url":null,"abstract":"Background: In the past decades, the rapid development of molecular biology has led to a generation of an unprecedented amount of biological data obtained by the scientific community. Therefore, there is a significant and unmet need to store, process, and make sense of such a vast amount of data. There are currently available a number of databases, that cover different fields of molecular biology. Objectives: In this paper, we describe Protein-Nucleic Acid Structural Database with Information on Accessible Surface Area, ProtNA-ASA, http://www.ire.kharkov.ua/ProtNA-ASA/index.php. The main aim of ProtNA-ASA is to provide quick and convenient access to structural information about DNA and protein-DNA complexes, that can be used for comprehensive study of protein-DNA recognition. Materials and Methods: ProtNA-ASA database comprise information based on X-ray or NMR structures derived from Nucleic Acids Data Bank: 973 structures of protein-DNA complexes, 129 structures of naked А- and 403 of B-DNA ones; following structural parameters for each structure: conformational DNA parameters calculated with the 3DNA/CompDNA analyzer; DNA accessible surface area calculated using the modified algorithm of Higo and Go; DNA electrostatic potential calculated with DelPhi package. Results: The recent update of ProtNA-ASA includes the electrostatic potential of the DNA minor groove since it plays an essential role in the indirect protein-DNA recognition process. The update also includes an advanced search, which serves to ease the use of the database and contribute to a more accurate structure selection. Advanced search allows finding structures by PDB/NDB ID, citation, length and sequence of a protein or DNA chain, type of structure, method of structure obtaining and resolution. All these queries can be used in different combinations with and/or statements. Conclusion: The combination of structural information and physical characteristics from the ProtNA-ASA database is particularly useful to scientists studying the indirect readout, that based on DNA deformability. The detail analyzes of protein-DNA complexes and mechanisms of protein-DNA recognition is essential for implications in understanding cellular processes, DNA metabolism, transcriptional regulation, and developing therapeutic drugs.","PeriodicalId":31658,"journal":{"name":"Biofizicnij Visnik","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135600336","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}