ISOB: A Database of Indigenous Snake Species of Bangladesh with respective known venom composition

Roly, Zahida Yesmin; Hakim, Abdul; Zahan, Asm Shahriar; Hossain, Moazzem; Reza, Abu

doi:10.6026/97320630011107

Cited by 15 publications

(14 citation statements)

References 19 publications

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“…A number of databases are available as a resource for venomics studies. The NCBI and Uniprot’s animal toxin annotation project databases offer a general resource of animal toxins, while a number of specifically focused databases are available and include potassium channel toxins (Kalium [ 58 ]), spiders (Arachnoserver [ 16 ]), cone snails (ConoServer [ 59 ]) and snakes of Bangladesh (ISOB [ 60 ]). As an example, Arachnoserver [ 16 ] acts as a specialised repository database of known and newly discovered spider venom peptides and proteins.…”

Section: Venomicsmentioning

confidence: 99%

Venomics: A Mini-Review

Wilson

Daly

2018

High-Throughput

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Venomics is the integration of proteomic, genomic and transcriptomic approaches to study venoms. Advances in these approaches have enabled increasingly more comprehensive analyses of venoms to be carried out, overcoming to some extent the limitations imposed by the complexity of the venoms and the small quantities that are often available. Advances in bioinformatics and high-throughput functional assay screening approaches have also had a significant impact on venomics. A combination of all these techniques is critical for enhancing our knowledge on the complexity of venoms and their potential therapeutic and agricultural applications. Here we highlight recent advances in these fields and their impact on venom analyses.

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Section: Venomicsmentioning

confidence: 99%

Venomics: A Mini-Review

Wilson

Daly

2018

High-Throughput

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“…Some aspects of toxin-centered databases were reviewed recently [ 24 ]. ConoServer ( ), ArachnoServer ( ), and ISOB (Indigenous Snake species Of Bangladesh, ) provide expert annotations on the sequences and 3D structures of cone snail, spider, and snake toxins, respectively [ 25 , 26 , 27 ]. There are currently no equivalent databases for other venomous species, and this absence has been noted as impeding venomics efforts [ 1 ].…”

Section: Databasesmentioning

confidence: 99%

“…Another important task of these two databases is to keep track of the rapidly evolving toxin classifications, which are frequently amended. In the remainder of this section we now give more information on the five most useful publicly available sources of data in venomics, namely ConoServer [ 25 , 31 ], ArachnoServer [ 26 , 32 ], ISOB [ 27 ], Tox-Prot [ 33 ] and ATDB (Animal Toxin DataBase) [ 34 ].…”

Section: Databasesmentioning

confidence: 99%

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Bioinformatics-Aided Venomics

Kaas

Craik

2015

Toxins

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Venomics is a modern approach that combines transcriptomics and proteomics to explore the toxin content of venoms. This review will give an overview of computational approaches that have been created to classify and consolidate venomics data, as well as algorithms that have helped discovery and analysis of toxin nucleic acid and protein sequences, toxin three-dimensional structures and toxin functions. Bioinformatics is used to tackle specific challenges associated with the identification and annotations of toxins. Recognizing toxin transcript sequences among second generation sequencing data cannot rely only on basic sequence similarity because toxins are highly divergent. Mass spectrometry sequencing of mature toxins is challenging because toxins can display a large number of post-translational modifications. Identifying the mature toxin region in toxin precursor sequences requires the prediction of the cleavage sites of proprotein convertases, most of which are unknown or not well characterized. Tracing the evolutionary relationships between toxins should consider specific mechanisms of rapid evolution as well as interactions between predatory animals and prey. Rapidly determining the activity of toxins is the main bottleneck in venomics discovery, but some recent bioinformatics and molecular modeling approaches give hope that accurate predictions of toxin specificity could be made in the near future.

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“…They are classified into two main superfamilies as enzymatic and non-enzymatic proteins. They are also classified into various toxin superfamilies and each superfamily contains wide arrays of several structurally distinct families of peptides those have diverse functions (Roly et al, 2015). Three-Finger Toxins (3FTxs) are one of the superfamily among some well characterized superfamilies of snake venom proteins.…”

Section: Introductionmentioning

confidence: 99%

Functional Characterization of Elapid Venom Toxin Proteins and Related Non-Toxin Proteins of Human through Comparative Analysis

Roly¹,

Ruhullah²,

Tanvir³

et al. 2015

Trends in Bioinformatics

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Snake venom contains a diverse array of pharmacologically active proteins and polypeptides that have led to the development of molecular probes and therapeutic agents. Short neurotoxins and cytotoxins are non-enzymatic polypeptides components of snake venom found only in the venoms of Elapidae (cobras, kraits, mambas, coral snakes and Australian elapids) and Hydrophidae (sea snakes). The three-dimensional structure of short neurotoxins and cytotoxins has three beta stranded loops resembling three-fingers of three-finger protein super family. This protein super family has different family members which are employed in various biological functions. The objective of this study is to search out the amino acid compositional (%) profile, physiochemical properties and functional analysis of three finger toxins present in different elapid snake species to be precise, Bungarus fasciatus, Naja naja and Naja kauthia. We analyzed a total of 23 reference protein sequences representing short neurotoxin and cytotoxin of three elapid snakes and related non-toxin proteins of human in terms of functional analysis, amino acid compositional (%) profile, number of amino acids, molecular weight, theoretical isoelectric point (pI), number of positively charged and negatively charged amino acid residues, instability index and grand average of hydropathy using computational tools. From the result it was found that amino acid composition profile represents that all sequences hold a conserved cysteine amount even as differential amount of different amino acid residues have a particular family pattern. It will also assist to know about involvement in various biological functions those are accountable for the vivid amino acid composition profile of these proteins. This comparative analysis of physicochemical properties would play a significant role in understanding the mechanisms of action of toxins and in the development of lead therapeutic molecules.

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ISOB: A Database of Indigenous Snake Species of Bangladesh with respective known venom composition

Cited by 15 publications

References 19 publications

Venomics: A Mini-Review

Venomics: A Mini-Review

Bioinformatics-Aided Venomics

Functional Characterization of Elapid Venom Toxin Proteins and Related Non-Toxin Proteins of Human through Comparative Analysis

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