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Journals Database : the Journal of Biol...

Database : the Journal of Biological Databases and Curation

https://read.qxmd.com/read/38537199/fopgdb-a-pangenome-database-of-fusarium-oxysporum-a-cross-kingdom-fungal-pathogen
#1
JOURNAL ARTICLE
Tan Meng, Hanqing Jiao, Yi Zhang, Yi Zhou, Shaoying Chen, Xinrui Wang, Bowen Yang, Jie Sun, Xin Geng, Dilay Hazal Ayhan, Li Guo
Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans...
March 27, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38537198/biokc-a-collaborative-platform-for-curation-and-annotation-of-molecular-interactions
#2
JOURNAL ARTICLE
Carlos Vega, Marek Ostaszewski, Valentin Grouès, Reinhard Schneider, Venkata Satagopam
Curation of biomedical knowledge into systems biology diagrammatic or computational models is essential for studying complex biological processes. However, systems-level curation is a laborious manual process, especially when facing ever-increasing growth of domain literature. New findings demonstrating elaborate relationships between multiple molecules, pathways and cells have to be represented in a format suitable for systems biology applications. Importantly, curation should capture the complexity of molecular interactions in such a format together with annotations of the involved elements and support stable identifiers and versioning...
March 27, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38531600/correction-to-sepdb-a-database-of-secreted-proteins
#3
(no author information available yet)
No abstract text is available yet for this article.
March 26, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38531599/esktides-a-comprehensive-database-and-mining-method-for-eskape-phage-derived-antimicrobial-peptides
#4
JOURNAL ARTICLE
Hongfang Wu, Rongxian Chen, Xuejian Li, Yue Zhang, Jianwei Zhang, Yanbo Yang, Jun Wan, Yang Zhou, Huanchun Chen, Jinquan Li, Runze Li, Geng Zou
'Superbugs' have received increasing attention from researchers, such as ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp.), which directly led to about 1 270 000 death cases in 2019. Recently, phage peptidoglycan hydrolases (PGHs)-derived antimicrobial peptides were proposed as new antibacterial agents against multidrug-resistant bacteria. However, there is still a lack of methods for mining antimicrobial peptides based on phages or phage PGHs...
March 26, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38502609/thermopcd-a-database-of-molecular-dynamics-trajectories-of-antibody-antigen-complexes-at-physiologic-and-fever-range-temperatures
#5
JOURNAL ARTICLE
Puneet K Singh, Razvan C Stan
Progression of various cancers and autoimmune diseases is associated with changes in systemic or local tissue temperatures, which may impact current therapies. The role of fever and acute inflammation-range temperatures on the stability and activity of antibodies relevant for cancers and autoimmunity is unknown. To produce molecular dynamics (MD) trajectories of immune complexes at relevant temperatures, we used the Research Collaboratory for Structural Bioinformatics (RCSB) database to identify 50 antibody:antigen complexes of interest, in addition to single antibodies and antigens, and deployed Groningen Machine for Chemical Simulations (GROMACS) to prepare and run the structures at different temperatures for 100-500 ns, in single or multiple random seeds...
March 19, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38502608/fgcd-a-database-of-fungal-gene-clusters-related-to-secondary-metabolism
#6
JOURNAL ARTICLE
Fuyuan Zhang, Hongzhe Cao, Helong Si, Jinping Zang, Jingao Dong, Jihong Xing, Kang Zhang
Fungal secondary metabolites are not necessary for growth, but they are important for fungal metabolism and ecology because they provide selective advantages for competition, survival and interactions with the environment. These various metabolites are widely used as medicinal precursors and insecticides. Secondary metabolism genes are commonly arranged in clusters along chromosomes, which allow for the coordinate control of complete pathways. In this study, we created the Fungal Gene Cluster Database to store, retrieve, and visualize secondary metabolite gene cluster information across fungal species...
March 19, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38507044/best-practices-for-the-manual-curation-of-intrinsically-disordered-proteins-in-disprot
#7
JOURNAL ARTICLE
Federica Quaglia, Anastasia Chasapi, Maria Victoria Nugnes, Maria Cristina Aspromonte, Emanuela Leonardi, Damiano Piovesan, Silvio C E Tosatto
The DisProt database is a resource containing manually curated data on experimentally validated intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) from the literature. Developed in 2005, its primary goal was to collect structural and functional information into proteins that lack a fixed three-dimensional structure. Today, DisProt has evolved into a major repository that not only collects experimental data but also contributes to our understanding of the IDPs/IDRs roles in various biological processes, such as autophagy or the life cycle mechanisms in viruses or their involvement in diseases (such as cancer and neurodevelopmental disorders)...
March 12, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38470883/aagingbase-a-comprehensive-database-of-anti-aging-peptides
#8
JOURNAL ARTICLE
Kunjulakshmi R, Ambuj Kumar, Keerthana Vinod Kumar, Avik Sengupta, Kavita Kundal, Simran Sharma, Ankita Pawar, Pithani Sai Krishna, Mohammad Alfatah, Sandipan Ray, Bhavana Tiwari, Rahul Kumar
The process of aging is an intrinsic and inevitable aspect of life that impacts every living organism. As biotechnological advancements continue to shape our understanding of medicine, peptide therapeutics have emerged as a promising strategy for anti-aging interventions. This is primarily due to their favorable attributes, such as low immunogenicity and cost-effective production. Peptide-based treatments have garnered widespread acceptance and interest in aging research, particularly in the context of age-related therapies...
March 12, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38459946/singleq-a-comprehensive-database-of-single-cell-expression-quantitative-trait-loci-sc-eqtls-cross-human-tissues
#9
JOURNAL ARTICLE
Zhiwei Zhou, Jingyi Du, Jianhua Wang, Liangyi Liu, M Gracie Gordon, Chun Jimmie Ye, Joseph E Powell, Mulin Jun Li, Shuquan Rao
Mapping of expression quantitative trait loci (eQTLs) and other molecular QTLs can help characterize the modes of action of disease-associated genetic variants. However, current eQTL databases present data from bulk RNA-seq approaches, which cannot shed light on the cell type- and environment-specific regulation of disease-associated genetic variants. Here, we introduce our Single-cell eQTL Interactive Database which collects single-cell eQTL (sc-eQTL) datasets and provides online visualization of sc-eQTLs across different cell types in a user-friendly manner...
March 9, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38345567/sepdb-a-database-of-secreted-proteins
#10
JOURNAL ARTICLE
Ruiqing Wang, Chao Ren, Tian Gao, Hao Li, Xiaochen Bo, Dahai Zhu, Dan Zhang, Hebing Chen, Yong Zhang
Detecting changes in the dynamics of secreted proteins in serum has been a challenge for proteomics. Enter secreted protein database (SEPDB), an integrated secretory proteomics database offering human, mouse and rat secretory proteomics datasets collected from serum, exosomes and cell culture media. SEPDB compiles secreted protein information from secreted protein database, UniProt and Human Protein Atlas databases to annotate secreted proteomics data based on protein subcellular localization and disease markers...
February 12, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38306294/araapp-filling-gaps-in-the-ecological-knowledge-of-spiders-using-an-automated-and-dynamic-approach-to-analyze-systematically-collected-community-data
#11
JOURNAL ARTICLE
Alexander Bach, Florian Raub, Hubert Höfer, Richard Ottermanns, Martina Roß-Nickoll
The ARAMOB data repository compiles meticulously curated spider community datasets from systematical collections, ensuring a high standard of data quality. These datasets are enriched with crucial methodological data that enable the datasets to be aligned in time and space, facilitating data synthesis across studies, respectively, collections. To streamline the analysis of these datasets in a species-specific context, a suite of tailored ecological analysis tools named ARAapp has been developed. By harnessing the capabilities of ARAapp, users can systematically evaluate the spider species data housed within the ARAMOB repository, elucidating intricate relationships with a range of parameters such as vertical stratification, habitat occurrence, ecological niche parameters (moisture and shading) and phenological patterns...
February 1, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38300518/nanolas-a-comprehensive-nanobody-database-with-data-integration-consolidation-and-application
#12
JOURNAL ARTICLE
Shuchang Xiong, Zhengwen Liu, Xin Yi, Kai Liu, Bingding Huang, Xin Wang
Nanobodies, a unique subclass of antibodies first discovered in camelid animals, are composed solely of a single heavy chain's variable region. Their significantly reduced molecular weight, in comparison to conventional antibodies, confers numerous advantages in the treatment of various diseases. As research and applications involving nanobodies expand, the quantity of identified nanobodies is also rapidly growing. However, the existing antibody databases are deficient in type and coverage, failing to satisfy the comprehensive needs of researchers and thus impeding progress in nanobody research...
January 31, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38284937/filling-knowledge-gaps-in-insect-conservation-by-leveraging-genetic-data-from-public-archives
#13
JOURNAL ARTICLE
Serena Baini, Alessio De Biase
Insect decline has become a growing concern in recent years, with studies showing alarming declines in populations of several taxa. Our knowledge about genetic spatial patterns and evolutionary history of insects still exhibits significant gaps hindering our ability to effectively conserve and manage insect populations and species. Genetic data may provide valuable insights into the diversity and the evolutionary relationships of insects' species and populations. Public repositories, such as GenBank and BOLD, containing vast archives of genetic data with associated metadata, offer an irreplaceable resource for researchers contributing to our understanding of species diversity, population structure and evolutionary relationships...
January 29, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38284936/ahp-db-a-reference-database-of-proteins-in-the-human-aqueous-humor
#14
JOURNAL ARTICLE
Tae Jin Lee, Arnav Goyal, Garrett Jones, Joshua Glass, Vishal Doshi, Kathryn Bollinger, Lane Ulrich, Saleh Ahmed, Sai Karthik Kodeboyina, Amy Estes, Marc Töteberg-Harms, Wenbo Zhi, Shruti Sharma, Ashok Sharma
The aqueous humor (AH) is a low-viscosity biofluid that continuously circulates from the posterior chamber to the anterior chamber of the eye. Recent advances in high-resolution mass-spectrometry workflows have facilitated the study of proteomic content in small-volume biofluids like AH, highlighting the potential clinical implications of the AH proteome. Nevertheless, in-depth investigations into the role of AH proteins in ocular diseases have encountered challenges due to limited accessibility to these workflows, difficulties in large-scale AH sample collection and the absence of a reference AH proteomic database...
January 29, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38245003/correction-to-the-importance-of-graph-databases-and-graph-learning-for-clinical-applications
#15
(no author information available yet)
No abstract text is available yet for this article.
January 20, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38245002/analysis-and-review-of-techniques-and-tools-based-on-machine-learning-and-deep-learning-for-prediction-of-lysine-malonylation-sites-in-protein-sequences
#16
JOURNAL ARTICLE
Shahin Ramazi, Seyed Amir Hossein Tabatabaei, Elham Khalili, Amirhossein Golshan Nia, Kiomars Motarjem
The post-translational modifications occur as crucial molecular regulatory mechanisms utilized to regulate diverse cellular processes. Malonylation of proteins, a reversible post-translational modification of lysine/k residues, is linked to a variety of biological functions, such as cellular regulation and pathogenesis. This modification plays a crucial role in metabolic pathways, mitochondrial functions, fatty acid oxidation and other life processes. However, accurately identifying malonylation sites is crucial to understand the molecular mechanism of malonylation, and the experimental identification can be a challenging and costly task...
January 19, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38242684/dapredict-a-database-for-drug-action-phenotype-prediction
#17
JOURNAL ARTICLE
Qingkang Meng, Yiyang Cai, Kun Zhou, Fei Xu, Diwei Huo, Hongbo Xie, Meini Yu, Denan Zhang, Xiujie Chen
The phenotypes of drug action, including therapeutic actions and adverse drug reactions (ADRs), are important indicators for evaluating the druggability of new drugs and repositioning the approved drugs. Here, we provide a user-friendly database, DAPredict (https://bio-bigdata.hrbmu.edu.cn/DAPredict), in which our novel original drug action phenotypes prediction algorithm (Yang,J., Zhang,D., Liu,L. et al. (2021) Computational drug repositioning based on the relationships between substructure-indication...
January 18, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38236197/an-optimized-relational-database-for-querying-structural-patterns-in-proteins
#18
JOURNAL ARTICLE
Renzo Angles, Mauricio Arenas-Salinas, Roberto García, Ben Ingram
A database is an essential component in almost any software system, and its creation involves more than just data modeling and schema design. It also includes query optimization and tuning. This paper focuses on a web system called GSP4PDB, which is used for searching structural patterns in proteins. The system utilizes a normalized relational database, which has proven to be inefficient even for simple queries. This article discusses the optimization of the GSP4PDB database by implementing two techniques: denormalization and indexing...
January 17, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38242685/correction-to-leishmaniadb-a-comparative-resource-for-leishmania-proteins
#19
(no author information available yet)
No abstract text is available yet for this article.
January 16, 2024: Database: the Journal of Biological Databases and Curation
https://read.qxmd.com/read/38227799/an-inflammatory-bowel-diseases-integrated-resources-portal-ibdirp
#20
JOURNAL ARTICLE
Nie Kai, Cai Qingsong, Ma Kejia, Luo Weiwei, Wu Xing, Chen Xuejie, Cai Lixia, Deng Minzi, Yang Yuanyuan, Wang Xiaoyan
IBD, including ulcerative colitis and Crohn's disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD. An integrated platform was developed that provides information on different aspects of IBD research resources, such as single-nucleotide polymorphisms (SNPs), genes, transcriptome, microbiota, metabolomics, single cells and other resources...
January 16, 2024: Database: the Journal of Biological Databases and Curation
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