Zobrazeno 1 - 10
of 29
pro vyhledávání: '"Thomas Litfin"'
Publikováno v:
RNA Biology, Vol 19, Iss 1, Pp 1179-1189 (2022)
Given the challenges for the experimental determination of RNA tertiary structures, probing solvent accessibility has become increasingly important to gain functional insights. Among various chemical probes developed, backbone-cleaving hydroxyl radic
Externí odkaz:
https://doaj.org/article/b23849d85bb84800bcd36b83e2a4e985
Publikováno v:
Scientific Reports, Vol 12, Iss 1, Pp 1-9 (2022)
Abstract Protein language models have emerged as an alternative to multiple sequence alignment for enriching sequence information and improving downstream prediction tasks such as biophysical, structural, and functional properties. Here we show that
Externí odkaz:
https://doaj.org/article/a1de07e4ee8b45c1b1d1fb4f88b98bf4
Publikováno v:
Genomics, Proteomics & Bioinformatics, Vol 17, Iss 6, Pp 645-656 (2019)
Intrinsically disordered or unstructured proteins (or regions in proteins) have been found to be important in a wide range of biological functions and implicated in many diseases. Due to the high cost and low efficiency of experimental determination
Externí odkaz:
https://doaj.org/article/cbfa6879abdc4fc6b9f3a37ecb7084bf
Publikováno v:
Computational and Structural Biotechnology Journal, Vol 17, Iss , Pp 1123-1134 (2019)
The covalent attachment of sugars to growing glycan chains is heavily reliant on a specific family of solute transporters (SLC35), the nucleotide sugar transporters (NSTs) that connect the synthesis of activated sugars in the nucleus or cytosol, to g
Externí odkaz:
https://doaj.org/article/cc77bde75bb447d3a87fba5f4bf20b3f
Autor:
John M. Atack, Chengying Guo, Thomas Litfin, Long Yang, Patrick J. Blackall, Yaoqi Zhou, Michael P. Jennings
Publikováno v:
mSystems, Vol 5, Iss 4 (2020)
ABSTRACT N6-Adenine DNA methyltransferases associated with some Type I and Type III restriction-modification (R-M) systems are able to undergo phase variation, randomly switching expression ON or OFF by varying the length of locus-encoded simple sequ
Externí odkaz:
https://doaj.org/article/91693bc9f96b4c51acd0bbffc06d674a
Publikováno v:
International Journal of Biological Macromolecules. 203:543-552
Splitting a protein at a position may lead to self- or assisted-complementary fragments depending on whether two resulting fragments can reconstitute to maintain the native function spontaneously or require assistance from two interacting molecules.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f1c88ccae059de1eb9aa04f03d9616e0
https://doi.org/10.1016/j.ijbiomac.2022.01.173
https://doi.org/10.1016/j.ijbiomac.2022.01.173
Autor:
Yikun Zhang, Mei Lang, Jiuhong Jiang, Zhiqiang Gao, Fan Xu, Thomas Litfin, Ke Chen, Jaswinder Singh, Xiansong Huang, Guoli Song, Yonghong Tian, Jian Zhan, Jie Chen, Yaoqi Zhou
Compared to proteins, DNA and RNA are more difficult languages to interpret because 4-letter-coded DNA/RNA sequences have less information content than 20-letter-coded protein sequences. While BERT (Bidirectional Encoder Representations from Transfor
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::ce892f6dd0814118b72cc21942580e0e
https://doi.org/10.1101/2023.03.15.532863
https://doi.org/10.1101/2023.03.15.532863
Recent success of AlphaFold2 in protein structure prediction relied heavily on co-evolutionary information derived from homologous protein sequences found in the huge, integrated database of protein sequences (Big Fantastic Database). In contrast, th
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::89b115ed1c3b2a81726699439c3cbd07
https://doi.org/10.1101/2023.02.01.526559
https://doi.org/10.1101/2023.02.01.526559
Unlike 20-letter-coded proteins, RNA homologous sequences are notoriously difficult to detect because their 4-letter-coded sequences can quickly lose their sequence identity. As a result, employing secondary structures has been found necessary to imp
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e355387642a263f271c72a051f03aae4
https://doi.org/10.1101/2022.10.03.510702
https://doi.org/10.1101/2022.10.03.510702
Publikováno v:
Bioinformatics. 37:3494-3500
Motivation The accuracy of RNA secondary and tertiary structure prediction can be significantly improved by using structural restraints derived from evolutionary coupling or direct coupling analysis. Currently, these coupling analyses relied on manua
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::89bab60b0f5fd1c9d4a095372c28cb34
https://doi.org/10.1093/bioinformatics/btab391
https://doi.org/10.1093/bioinformatics/btab391