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A review on antimicrobial peptides databases and the computational tools
AbstractAntimicrobial Peptides (AMPs) have been considered as potential alternatives for infection therapeutics since antibiotic resistance has been raised as a global problem. The AMPs are a group of natural peptides that play a crucial role in the immune system in various organisms AMPs have features such as a short length and efficiency against microbes. Importantly, they have represented low toxicity in mammals which makes them potential candidates for peptide-based drugs. Nevertheless, the discovery of AMPs is accompanied by several issues which are associated with labour-intensive and time-consuming wet-lab experimen...
Source: Database : The Journal of Biological Databases and Curation - March 19, 2022 Category: Databases & Libraries Source Type: research

Halophytes.tn: an innovative database for Tunisian halophyte plant identification, distribution and characterization
We describe the practical and technical steps followed and bi oinformatics tools used to conceive and design the first Tunisian halophytes database, enabling species identification and characterization. As a first version, information about botany, morphology, ecophysiology and biochemistry were provided for the identified species with their sites of growing i n Tunisia, first step of biodiversity conservation, management and valorization. The database will be regularly maintained, updated and enriched to achieve the goal of whole Tunisian halophyte species and fit the needs of scientists and all category of users.Database...
Source: Database : The Journal of Biological Databases and Curation - March 19, 2022 Category: Databases & Libraries Source Type: research

Correction to: FEDA (Food Enzyme Database): a web application gathering information about food enzyme preparations available on the European market
(Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - March 19, 2022 Category: Databases & Libraries Source Type: research

MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer
AbstractMicroRNA childhood Cancer Catalog (M3Cs) is a high-quality curated collection of published miRNA research studies on 16 pediatric cancer diseases. M3Cs scope was based on two approaches: data-driven clinical significance and data-driven human pediatric cell line models. Based on the translational bioinformatics spectrum, the main objective of this study is to bring miRNA research into clinical significance in both pediatric cancer patient care and drug discovery toward health informatics in childhood cancer. M3Cs development passed through three phases: 1. Literature Mining: It includes external database search and...
Source: Database : The Journal of Biological Databases and Curation - March 18, 2022 Category: Databases & Libraries Source Type: research

HPVMD-C: a disease-based mutation database of human papillomavirus in China
AbstractHuman papillomavirus (HPV) can cause condyloma acuminatum and cervical cancer. Some mutations of these viruses are closely related to the persistent infection of cervical cancer and are ideal cancer vaccine targets. Several databases have been developed to collect HPV sequences, but no HPV mutation database has been published. This paper reports a Chinese HPV mutation database (HPVMD-C), which contains 149 HPV genotypes, 468 HPV mutations, 3409 protein sequences, 4727 domains and 236 epitopes. We analyzed the mutation distribution among HPV genotypes, domains and epitopes. We designed a visualization tool to displa...
Source: Database : The Journal of Biological Databases and Curation - March 14, 2022 Category: Databases & Libraries Source Type: research

ImmuneData: an integrated data discovery system for immunology data repositories
AbstractTo meet the increasing demand for data sharing, data reuse and meta-analysis in the immunology research community, we have developed the data discovery system ImmuneData. The system provides integrated access to five immunology data repositories funded by the National Institute of Allergy and Infectious Diseases, Division of Allergy, Immunology and Transplantation, including ImmPort, ImmuneSpace, ITN TrialShare, ImmGen and IEDB. ImmuneData restructures the data repositories ’ metadata into a uniform schema using domain experts’ knowledge and state-of-the-art Natural Language Processing (NLP) technologies. It co...
Source: Database : The Journal of Biological Databases and Curation - March 9, 2022 Category: Databases & Libraries Source Type: research

PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation
AbstractThe number of publications reporting putative plastic-degrading microbes and proteins is continuously increasing, necessitating the compilation of these data and the development of tools to facilitate their analysis. We developed the PlasticDB web application to address this need, which comprises a database of microorganisms and proteins reported to biodegrade plastics. Associated metadata, such as the techniques utilized to assess biodegradation, the environmental source of microbial isolate and presumed thermophilic traits are also reported. Proteins in the database are categorized according to the plastic type t...
Source: Database : The Journal of Biological Databases and Curation - March 9, 2022 Category: Databases & Libraries Source Type: research

FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research
In conclusion, FibROAD serves as a convenient platform where researchers can acquire integrated evidence and a more comprehensive understanding of fibrosis-related disorders.Database URL https://www.fibroad.org (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - March 9, 2022 Category: Databases & Libraries Source Type: research

Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase
This study highlights the potential of pathway databases such as Reactome in modeling genetic perturbations, promoting standardization of experimental pathway activity readout and supporting hypothesis-driven research by revealing relationships between pathway inputs and outputs that have not yet been directly experimentally tested.Database URLwww.reactome.org (Source: Database : The Journal of Biological Databases and Curation)
Source: Database : The Journal of Biological Databases and Curation - March 6, 2022 Category: Databases & Libraries Source Type: research

Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins
AbstractWe previously released the Anti-CRISPRdb database hosting anti-CRISPR proteins (Acrs) and associated information. Since then, the number of known Acr families, types, structures and inhibitory activities has accumulated over time, and Acr neighbors can be used as a candidate pool for screening Acrs in further studies. Therefore, we here updated the database to include the new available information. Our newly updated database shows several improvements: (i) it comprises more entries and families because it includes both Acrs reported in the most recent literatures and Acrs obtained via performing homologous alignmen...
Source: Database : The Journal of Biological Databases and Curation - March 4, 2022 Category: Databases & Libraries Source Type: research

PSINDB: the postsynaptic protein –protein interaction database
AbstractThe postsynaptic region is the receiving part of the synapse comprising thousands of proteins forming an elaborate and dynamically changing network indispensable for the molecular mechanisms behind fundamental phenomena such as learning and memory. Despite the growing amount of information about individual protein –protein interactions (PPIs) in this network, these data are mostly scattered in the literature or stored in generic databases that are not designed to display aspects that are fundamental to the understanding of postsynaptic functions. To overcome these limitations, we collected postsynaptic PPIs compl...
Source: Database : The Journal of Biological Databases and Curation - March 2, 2022 Category: Databases & Libraries Source Type: research

Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank
AbstractRapid response to the current coronavirus disease 2019 (COVID-19) pandemic requires fast dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequence data in order to align diagnostic tests and vaccines with the natural evolution of the virus as it spreads through the world. To facilitate this, the National Library of Medicine ’s National Center for Biotechnology Information developed an automated pipeline for the deposition and quick processing of SARS-CoV-2 genome assemblies into GenBank for the user community. The pipeline ensures the collection of contextual information about...
Source: Database : The Journal of Biological Databases and Curation - March 1, 2022 Category: Databases & Libraries Source Type: research

DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins
AbstractDisulphide bonds are stabilizing crosslinks in proteins and serve to enhance their thermal stability. In proteins that are small and rich in disulphide bonds, they could be the major determining factor for the choice of conformational state since their constraints on appropriate backbone conformation can be substantial. Such crosslinks and their positional conservation could itself enable protein family and functional association. Despite the importance of the field, there is no comprehensive database on disulphide crosslinks that is available to the public. Herein we provide information on disulphides in DSDBASE2....
Source: Database : The Journal of Biological Databases and Curation - March 1, 2022 Category: Databases & Libraries Source Type: research

GNIFdb: a neoantigen intrinsic feature database for glioma
AbstractAbstractNeoantigens are mutation-containing immunogenic peptides from tumor cells. Neoantigen intrinsic features are neoantigens ’ sequence-associated features characterized by different amino acid descriptors and physical–chemical properties, which have a crucial function in prioritization of neoantigens with immunogenic potentials and predicting patients with better survival. Different intrinsic features might have func tions to varying degrees in evaluating neoantigens’ potentials of immunogenicity. Identification and comparison of intrinsic features among neoantigens are particularly important for develop...
Source: Database : The Journal of Biological Databases and Curation - February 12, 2022 Category: Databases & Libraries Source Type: research

DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development
AbstractDrug-likeness is a vital consideration when selecting compounds in the early stage of drug discovery. A series of drug-like properties are needed to predict the drug-likeness of a given compound and provide useful guidelines to increase the likelihood of converting lead compounds into drugs. Experimental physicochemical properties, pharmacokinetic/toxicokinetic properties and maximum dosages of approved small-molecule drugs from multiple text-based unstructured data resources have been manually assembled, curated, further digitized and processed into structured data, which are deposited in the Database of Digital P...
Source: Database : The Journal of Biological Databases and Curation - February 7, 2022 Category: Databases & Libraries Source Type: research