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Venom or zootoxin is a type of toxin produced by an animal that is actively delivered through a wound by means of a bite, sting, or similar action. The toxin is delivered through a specially evolved venom apparatus, such as fangs or a stinger, in a process called envenomation. Venom is often distinguished from poison, which is a toxin that is passively delivered by being ingested, inhaled, or absorbed through the skin, and toxungen, which is actively transferred to the external surface of another animal via a physical delivery mechanism.
The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases
Amos Bairoch is a Swiss bioinformatician and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, curation, and experimental efforts to functionally characterize human proteins.
The Pathogen-Host Interactions database (PHI-base) is a biological database that contains manually curated information on genes experimentally proven to affect the outcome of pathogen-host interactions. The database has been maintained by researchers at Rothamsted Research and external collaborators since 2005. PHI-base has been part of the UK node of ELIXIR, the European life-science infrastructure for biological information, since 2016.
Therapeutic Target Database (TTD) is a pharmaceutical and medical repository constructed by the Innovative Drug Research and Bioinformatics Group (IDRB) at Zhejiang University, China and the Bioinformatics and Drug Design Group at the National University of Singapore. It provides information about known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Detailed knowledge about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, and clinical development status. TTD is freely accessible without any login requirement at https://idrblab.org/ttd/.
Bacterial small RNAs are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.
A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
BmKAEP is a neurotoxin from the venom of the Manchurian scorpion (Mesobuthus martensii). It is a β-toxin, which shift the activation voltage of sodium channels towards more negative potentials.
OMPdb is a dedicated database that contains beta barrel (β-barrel) outer membrane proteins from Gram-negative bacteria. Such proteins are responsible for a broad range of important functions, like passive nutrient uptake, active transport of large molecules, protein secretion, as well as adhesion to host cells, through which bacteria expose their virulence activity.
DisProt is a manually curated biological database of intrinsically disordered proteins (IDPs) and regions (IDRs). DisProt annotations cover state information on the protein but also, when available, its state transitions, interactions and functional aspects of disorder detected by specific experimental methods. DisProt is hosted and maintained in the BioComputing UP laboratory.
The Multi-Omics Profiling Expression Database (MOPED) was an expanding multi-omics resource that supports rapid browsing of transcriptomics and proteomics information from publicly available studies on model organisms and humans. As to date (2021) it has ceased activities and is unaccessible online.
Donna R. Maglott is a staff scientist at the National Center for Biotechnology Information known for her research on large-scale genomics projects, including the mouse genome and development of databases required for genomics research.
In molecular biology, MobiDB is a curated biological database designed to offer a centralized resource for annotations of intrinsic protein disorder. Protein disorder is a structural feature characterizing a large number of proteins with prominent members known as intrinsically unstructured proteins. The database features three levels of annotation: manually curated, indirect and predicted. By combining different data sources of protein disorder into a consensus annotation, MobiDB aims at giving the best possible picture of the "disorder landscape" of a given protein of interest.
VFDB also known as Virulence Factor Database is a database that provides scientist quick access to virulence factors in bacterial pathogens. It can be navigated and browsed using genus or words. A BLAST tool is provided for search against known virulence factors. VFDB contains a collection of 16 important bacterial pathogens. Perl scripts were used to extract positions and sequences of VF from GenBank. Clusters of Orthologous Groups (COG) was used to update incomplete annotations. More information was obtained by NCBI. VFDB was built on Linux operation systems on DELL PowerEdge 1600SC servers.
CBMAR otherwise known as Comprehensive β-lactamase Molecular Annotation Resource is a database focused on the annotation and discovery of novel beta-lactamase genes and proteins in bacteria. Beta-lactamases are characterized on CBMAR using the Ambler Classification system. CBMAR organizes beta-lactamases according to their classes: A, B, C, and D. They are then further categorized by their (i) sequence variability, (ii) antibiotic resistance profile, (iii) inhibitor susceptibility, (iv) active site, (v) family fingerprints, (vi) mutational profile, (vii) variants, (viii) gene location, (ix) phylogenetic tree, etc. The primary sources of database for CBMAR are GenBank and Uniprot. CBMAR is built on an Apache HTTP Server 2.2.17 with MySQL Ver 14.14 and hosted on Ubuntu 11.04 Linux platform.
Ivan Erill is a Spanish computational biologist known for his research in comparative genomics and molecular microbiology. His work focuses primarily on bacterial comparative genomics, through the development of computational methods for analyzing regulatory networks and their evolution.
Tb1 is a neurotoxin that is naturally found in the venom of the Brazilian scorpion Tityus bahiensis. Presumably by acting on voltage-gated sodium channels, it triggers excessive glutamate release, which can lead to both behavioral and electrographic epileptiform alterations, as well as neuronal injury.
κ-KTx2.5 is a toxin found in the venom of the scorpion, Opisthacanthuscayaporum. The toxin belongs to the κ-KTx family, a channel blocker family that targets voltage-gated potassium channels (Kv) 1.1 and 1.4.
References
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- ↑ Jungo, Florence; Bairoch, Amos (March 2005). "Tox-Prot, the toxin protein annotation program of the Swiss-Prot protein knowledgebase". Toxicon. 45 (3): 293–301. doi:10.1016/j.toxicon.2004.10.018. ISSN 0041-0101. PMID 15683867.
- ↑ Srinivasan, K.N.; Gopalakrishnakone, P.; Tan, P.T.; Chew, K.C.; Cheng, B.; Kini, R.M.; Koh, J.L.Y.; Seah, S.H.; Brusic, V. (January 2002). "SCORPION, a molecular database of scorpion toxins". Toxicon. 40 (1): 23–31. doi:10.1016/s0041-0101(01)00182-9. ISSN 0041-0101. PMID 11602275.
- ↑ "Author Index Vol. 15, No. 1, 2008". Journal of Molecular Microbiology and Biotechnology. 15 (1): 65. 2008. doi: 10.1159/000121450 . ISSN 1464-1801.
- ↑ Attwood, Teresa K.; Bradley, Paul M.; Gaulton, Anna; Maudling, Neil; Mitchell, Alexander L.; Moulton, Georgina (2005-04-15), "The PRINTS protein fingerprint database: functional and evolutionary applications", Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons, Ltd, doi:10.1002/047001153x.g306301, ISBN 047001153X
- ↑ Chen, L. (2004-12-17). "VFDB: a reference database for bacterial virulence factors". Nucleic Acids Research. 33 (Database issue): D325–D328. doi:10.1093/nar/gki008. ISSN 1362-4962. PMC 539962 . PMID 15608208.
- ↑ Mantri, Y. (2004-01-01). "Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities". Nucleic Acids Research. 32 (90001): 55D–58. doi:10.1093/nar/gkh059. ISSN 1362-4962. PMC 308793 . PMID 14681358.
- ↑ Scaria, Joy; Chandramouli, Umamaheswaran; Verma, Sanjay Kumar (2005-02-01). "Antibiotic Resistance Genes Online (ARGO): A Database on vancomycin and b-lactam resistance genes". Bioinformation. 1 (1): 5–7. doi: 10.6026/97320630001005 . ISSN 0973-8894. PMC 1891619 . PMID 17597841.
- ↑ Yeats, C.; Lees, J.; Reid, A.; Kellam, P.; Martin, N.; Liu, X.; Orengo, C. (2007-12-23). "Gene3D: comprehensive structural and functional annotation of genomes". Nucleic Acids Research. 36 (Database): D414–D418. doi: 10.1093/nar/gkm1019 . ISSN 0305-1048. PMC 2238970 . PMID 18032434.