The 2023 <i>Nucleic Acids Research</i> Database Issue and the online molecular biology database collection

Rigden, Daniel J.; Fernández, Xosé M.

doi:10.1093/nar/gkac1186

Cited by 24 publications

(23 citation statements)

References 151 publications

(148 reference statements)

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“…Significant information about the DNA nucleotide sequences and amino acid sequences of proteins, obtained from different laboratories worldwide, is currently available in different database repositories [1,3]. These biological databases are utilized in genetic engineering of biological systems to increase the production of desired products or chemicals for benefit of plants and animals [4,6].…”

Section: Discussionmentioning

confidence: 99%

“…Digitalized biological information and databases are doubling after every 12 to 18 months with current advances in genomics and proteomics [1]. Recently, there has been enormous progress in unraveling the complexities of naturally-occurring biological systems, which has provided abundant scientific information in the field of nucleic acid sequences and protein databases for agriculture, biomedical research, synthetic biology (biological and chemical engineering), and metabolic engineering including production of pharmaceuticals and nutraceuticals (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Biological Databases and Resources: Their Engineering and Applications in Synthetic Biology

Sindhu¹,

Sindhu²

2023

IJASE

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Biological sciences pose a unique set of engineering challenges due to incomplete understanding of natural biological systems. Currently, sequencing of macromolecules i.e., DNA (deoxyribose nucleic acid) and proteins obtained from living cells has provided significant information, which is available in different database repositories. These databases comprising of genomic sequences and amino acid sequences (proteins) are utilized in genetic engineering of biological systems to increase the production of chemicals and pharmaceuticals for improving plant and animal health. Recently, synthetic biology approaches are being employed in rational and highthroughput biological engineering to enhance the production of beneficial chemicals. Recent molecular and bioinformatics tools have enabled to redesign the entire biological cycle, including construction of synthetic DNA inside the cell or replacement of entire genome to create synthetic organisms by utilizing gene libraries, computational tools and interfaces. This review describes the genomic, proteomic and phylogenetic databases, which may be utilized for designing and manipulation of synthetic gene circuits to perform novel functions and desired phenotypes in different ecosystems. In addition, synthetic biology approaches were discussed for designing biological systems for production and release of specific metabolic products. The progress and challenges faced in computational methodology and synthetic biology approaches are discussed for their potential applications in synthetic biology.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Biological Databases and Resources: Their Engineering and Applications in Synthetic Biology

Sindhu¹,

Sindhu²

2023

IJASE

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“…A module detection algorithm (M1) was applied to the network using the MOdularising NEtwork Toolbox that adopts a multiresolution approach to combine optimization algorithms to improve modularity [90]. Enrichment analyses Pathway enrichment analysis was performed using g:profiler (https://biit.cs.ut.ee/gprofiler/gost, [91]), a public webserver using Ensembl and Ensembl Genomes to identify significantly enriched terms in Gene Ontology (GO) biological processes, KEGG and Reactome databases [92–94]. Pathways were ranked by significance (p<0.01) and the most significant term per database for the protein or each module was taken as the representative pathway.…”

Section: Methodsmentioning

confidence: 99%

“…Pathway enrichment analysis was performed using g:profiler (https://biit.cs.ut.ee/gprofiler/gost, [91]), a public webserver using Ensembl and Ensembl Genomes to identify significantly enriched terms in Gene Ontology (GO) biological processes, KEGG and Reactome databases [92–94]. Pathways were ranked by significance (p<0.01) and the most significant term per database for the protein or each module was taken as the representative pathway.…”

Section: Methodsmentioning

confidence: 99%

Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

Waman,

Ashford,

Lam

et al. 2023

Preprint

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The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection. Ostensibly, certain populations or clinical groups may be more vulnerable. Factors causing these differences are unclear and whilst socioeconomic and cultural differences are likely to be important, human genetic factors could influence susceptibility. Experimental studies indicate SARS-CoV-2 uses innate immune suppression as a strategy to speed-up entry and replication into the host cell. Therefore, it is necessary to understand the impact of variants in immunity-associated human proteins on susceptibility to COVID-19.In this work, we analysed missense coding variants in several SARS-CoV-2 proteins and its human protein interactors that could enhance binding affinity to SARS-CoV-2. We curated a dataset of 19 SARS-CoV-2: human protein 3D-complexes, from the experimentally determined structures in the Protein Data Bank and models built using AlphaFold2-multimer, and analysed impact of missense variants occurring in the protein-protein interface region. We analysed 468 missense variants from human proteins and 212 variants from SARS-CoV-2 proteins and computationally predicted their impacts on binding affinities to SARS-CoV-2 proteins, using 3D-complexes.We predicted a total of 26 affinity-enhancing variants from 14 human proteins implicated in increased binding affinity to SARS-CoV-2. These include key-immunity associated genes (TOMM70, ISG15, IFIH1, IFIT2, RPS3, PALS1, NUP98, RAE1, AXL, ARF6, TRIMM, TRIM25) as well as important spike receptors (KREMEN1, AXL and ACE2). We report both common (e.g., Y13N in IFIH1) and rare variants in these proteins and discuss their likely structural and functional impact, using information on known and predicted functional sites. Potential mechanisms associated with immune suppression implicated by these variants are discussed.Occurrence of certain predicted affinity-enhancing variants should be monitored as they could lead to increased susceptibility and reduced immune response to SARS-CoV-2 infection in individuals/populations carrying them. Our analyses aid in understanding the potential impact of genetic variation in immunity-associated proteins on COVID-19 susceptibility and help guide drug-repurposing strategies.

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“…Figure 1. Comparison of five catalogs content: (1) re3data.org, (2) FAIRsharing [23], (3) The Database Commons [24], (4) ELIXIR bio.tools[25], and (5) NAR database list[26]. Among all up-to-date virus-specific databases, they were categorized into three groups: inclusion in our curated Table1, exclusive focus on coronavirus (see TableS4), or non-corona-related databases mentioned in the text; see Section 2.4.…”

mentioning

confidence: 99%

Navigating the Landscape: A Comprehensive Review of Current Virus Databases

Ritsch¹,

Cassman²,

Saghaei³

et al. 2023

Preprint

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Viruses are abundant and diverse entities that have important roles in public health, ecology, and agriculture. Identification and surveillance of viruses rely on understanding their genome organization, sequences, and replication strategy. Despite technological advancements in sequencing methods, our current understanding of virus diversity remains incomplete, highlighting the need to explore undiscovered viruses. Virus databases play a crucial role in providing access to sequences, annotations and other metadata, and analysis tools for studying viruses. However, there has not been a comprehensive review of virus databases in the last five years. This study aimed to fill this gap by identifying 24 active virus databases and included an extensive evaluation of their content, functionality and compliance with the FAIR principles. In this study, we thoroughly assessed the search capabilities of five database catalogs, which serve as comprehensive repositories housing a diverse array of databases and offering essential metadata. Moreover, we conducted a comprehensive review of different types of errors, encompassing taxonomy, names, missing information, sequences, sequence orientation, and chimeric sequences, with the intention of empowering users to effectively tackle these challenges. We expect this review to aid users in selecting suitable virus databases and other resources, and to help databases in error management and improve their adherence to the FAIR principles. The databases listed here represent current knowledge of viruses and will help aid users find databases of interest based on content, functionality, and scope. Use of virus databases is integral to gain new insights into the biology, evolution, and transmission of viruses, and develop new strategies to manage virus outbreaks and preserve global health.

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The 2023 Nucleic Acids Research Database Issue and the online molecular biology database collection

Cited by 24 publications

References 151 publications

Biological Databases and Resources: Their Engineering and Applications in Synthetic Biology

Biological Databases and Resources: Their Engineering and Applications in Synthetic Biology

Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics

Navigating the Landscape: A Comprehensive Review of Current Virus Databases

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