Homology modelling

This study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds.

16p vinarcissa 21-03-2023 5 1   Download

Expression of the CNDP2 gene is frequently up- or down-regulated in different types of human cancers. However, how the product of this gene is involved in cell growth and proliferation is poorly understood. Moreover, our knowledge of the functions of the CNDP2 orthologs in well-established model organisms is scarce.

9p vihagrid 30-01-2023 4 3   Download

With the introduction of DNA-damaging therapies into standard of care cancer treatment, there is a growing need for predictive diagnostics assessing homologous recombination deficiency (HRD) status across tumor types. Following the strong clinical evidence for the utility of DNA-sequencing-based HRD testing in ovarian cancer, and growing evidence in breast cancer, we present analytical validation of the Tempus HRD-DNA test.

17p visusanwojcicki 28-06-2022 12 2   Download

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome’s organization.

22p vialfrednobel 29-01-2022 14 0   Download

The CRISPR-Cas9 system is a widely utilized platform for transgenic animal production in various species, although its off-target effects should be addressed. Several applications of this tool have been proposed in model animals but remain insufficient for transgenic livestock production.

15p vialfrednobel 29-01-2022 5 1   Download

Conditional knockout mice and transgenic mice expressing recombinases, reporters, and inducible transcriptional activators are key for many genetic studies and comprise over 90% of mouse models created. Conditional knockout mice are generated using labor-intensive methods of homologous recombination in embryonic stem cells and are available for only ~25% of all mouse genes.

15p vialfrednobel 29-01-2022 14 0   Download

Nanopore sequencing has been widely used for the reconstruction of microbial genomes. Owing to higher error rates, errors on the genome are corrected via neural networks trained by Nanopore reads. However, the systematic errors usually remain uncorrected. This paper designs a model that is trained by homologous sequences for the correction of Nanopore systematic errors.

17p viarchimedes 26-01-2022 13 0   Download

Optimal functionality of synthetic lung surfactant for treatment of respiratory distress syndrome in preterm infants largely depends on the quality and quantity of the surfactant protein B (SP-B) peptide mimic and the lipid mixture.

12p vimackenziebezos 29-11-2021 6 1   Download

Leucine decarboxylase (LDC) is a recently proposed enzyme with no official enzyme commission number yet. It is encoded by the Mus musculus gene Gm853 which is expressed at kidneys, generating isopentylamine, an alkylmonoamine that has not been described to be formed by any metazoan enzyme yet. Although the relevance of LDC in mammalian physiology has not been fully determined, isopentylamine is a potential modulator which may have effects on insulin secretion and healthy gut microbiota formation.

16p tudichquannguyet 29-11-2021 4 1   Download

The selectivity and the thermostability of EndoBI-1 and EndoBI-2 suggest that these enzymes may be useful for many scientific and industrial applications. In this study, the growing numbers of homologous sequences in different databases were exploited in a comparative approach to investigate structural properties of EndoBI-1 and EndoBI-2 enzymes. Moreover, the complete and partial homology models of these two enzymes were generated and evaluated.

13p tudichquannguyet 29-11-2021 8 2   Download

Drosophila model is intensively studied for the development of cancer. The diminutive (dMyc), a homolog of the human MYC gene, is responsible for cell- apoptosis and its upregulation is responsible for determining the fate of cancerous growth in humans and Drosophila model. This work implores the requirement of dMyc and its expression as one of the major regulator of cancer with other proteins and repression of dMyc mRNA in Drosophila S2 cells.

7p thiencuuchu 27-11-2021 13 1   Download

A large number of disease resistance genes or QTLs in crop plants are identified through conventional genetics and genomic tools, but their functional or molecular characterization remains costly, labor-intensive and inaccurate largely due to the lack of deep sequencing of large and complex genomes of many important crops such as allohexaploid wheat (Triticum aestivum L.). On the other hand, gene annotation and relevant genomic resources for disease resistance and other defense-related traits are more abundant in model plant Arabidopsis (Arabidopsis thaliana).

13p vilarryellison 29-10-2021 12 0   Download

Nicotiana benthamiana is an important model organism of the Solanaceae (Nightshade) family. Several draft assemblies of the N. benthamiana genome have been generated, but many of the gene-models in these draft assemblies appear incorrect.

15p visilicon2711 20-08-2021 12 1   Download

Structural homology modeling supported by bioinformatics analysis plays a key role in uncovering new molecular interactions within gene regulatory networks. Here, we have applied this powerful approach to analyze the molecular interactions orchestrating death receptor signaling networks.

12p visilicon2711 20-08-2021 16 1   Download

Gene targeting by homology-directed repair (HDR) can precisely edit the genome and is a versatile tool for biomedical research. However, the efficiency of HDR-based modification is still low in many model organisms including zebrafish.

12p vijeeni2711 24-07-2021 10 0   Download

Female infertility is a worldwide concern and the etiology of infertility has not been thoroughly demonstrated. Although the mouse is a good model system to perform functional studies, the differences between mouse and human also need to be considered.

11p vijeeni2711 24-07-2021 16 0   Download

The fungus Parastagonospora nodorum causes septoria nodorum blotch (SNB) of wheat (Triticum aestivum) and is a model species for necrotrophic plant pathogens. The genome assembly of reference isolate Sn15 was first reported in 2007.

16p vilichoo2711 23-06-2021 6 1   Download

Src homology 2 containing protein tyrosine phosphatase (PTP) 2 (Shp2) is a typical tyrosine phosphatase interacting with receptor tyrosine kinase to regulate multiple signaling pathways in diverse pathological processes. Here, we will investigate the effect of Shp2 inhibition on pulmonary arterial hypertension (PAH) in a rat model and its potential cellular and molecular mechanisms underlying.

10p vimontana2711 05-04-2021 11 3   Download

In this study, we conducted cytotoxicity assay of 7 ent-kaurane diterpenoids from Croton tonkinensis against HepG2 cancer cell line. Homology modeling was used to determine the 3D structure of mortalin and p53 crystal structure involved mortalin-binding site was selected. All studied compounds were submitted for molecular docking to investigate inhibition mechanism of bioactive compounds.

9p nguaconbaynhay11 01-04-2021 10 2   Download

Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is challenging to obtain structures more accurate than the single best templates by either combining information from multiple templates or by modeling regions that vary among templates or are not covered by any templates.

8p viwyoming2711 16-12-2020 10 0   Download