Web resources, databases, and tools
commonly used in venom and toxin-related research



This table is the result of collaborative work by the EUVEN COST Action web resource group and is published in Zancolli et al. (2024) as table S1.

This table is designed to evolve. If you have suggestions for adding or modifying links, please send them to the contact address.

Web resource URL Description
Venom and toxin specific
ArachnoServer https://arachnoserver.qfab.org/mainMenu.html DB and prediction tools of spider toxins
ConoServer http://www.conoserver.org/ DB and prediction tools of cone snail toxins
UniProtKB/Swiss-Prot Tox-Prot https://www.uniprot.org/program/Toxins DB of venom proteins from all taxa
VenomZone https://venomzone.expasy.org/ Webportal with information on venoms from major venomous taxa
T3DB http://www.t3db.ca CURRENTLY UNAVAILABLE - DB of toxin data and target information, and tools for toxin metabolism and toxin/drug interaction predictions
ToxDL http://www.csbio.sjtu.edu.cn/bioinf/ToxDL/ Protein toxicity predictor with deep learning
ToxinPred https://webs.iiitd.edu.in/raghava/toxinpred/index.html Peptide toxicity predictor and tool for predicting toxicity of peptides and small proteins and designing peptides with desired toxicity
ToxinPred2 https://webs.iiitd.edu.in/raghava/toxinpred2/ Toxin predictor and tool for predicting the toxicity of proteins
ToxinPred3 https://webs.iiitd.edu.in/raghava/toxinpred3/ Upgraded version of ToxinPred, peptide toxicity predictor and tool for predicting toxicity of peptides and small proteins
VenoMS https://www.venoms.ch Low molecular mass spider toxin database
ToxClassifier http://bioserv7.bioinfo.pbf.hr/ToxClassifier/ CURRENTLY UNAVAILABLE - Toxin predictor
VenomKB http://venomkb.tatonettilab.org CURRENTLY UNAVAILABLE - Knowledgebase for aggregating and identifying therapeutic uses of animal venoms and venom compounds
Raw data repositories
DDBJ https://www.ddbj.nig.ac.jp Nucleotide sequencing data (DNA databank of Japan)
DDBJ https://www.ddbj.nig.ac.jp/dra/ Sequence Read Archive (SRA) data
ENA https://www.ebi.ac.uk/ena/browser/home Nucleotide sequencing data (European Nucleotide Archive)
GenBank https://ncbi.nlm.nih.gov/genbank/ Nucleotide sequencing data
GenBank https://ncbi.nlm.nih.gov/sra/ Sequence Read Archive (SRA) data
MassiVE https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp Mass spectrometry proteomics data
PRIDE https://www.ebi.ac.uk/pride/ Mass spectrometry proteomics data
PASSEL https://peptideatlas.org/passel/ Selected reaction monitoring (SRM/MRM) data
PDBe https://www.ebi.ac.uk/pdbe/deposition-services 3D macromolecular structures and EM volume maps
BMRB https://bmrb.io Various kinds of Data including nuclear magnetic resonance spectroscopy data, X-ray, electron microscopy, etc
EMDB https://www.ebi.ac.uk/emdb/ Repository for cryogenic-sample Electron Microscopy (cryoEM) volumes and representative tomograms of macromolecular complexes and subcellular structures
Genes, proteins, and other compounds
UniProtKB https://www.uniprot.org/ Comprehensive resource for protein sequence and annotation data curated by the EMBL-EBI, SIB and PIR
NCBI Nucleotide https://www.ncbi.nlm.nih.gov/nuccore Collection of sequences from several sources, including Genbank, RefSeq, TPA and PDB
NCBI RefSeq https://www.ncbi.nlm.nih.gov/refseq/ Set of reference sequences including genomic, transcript, and protein. Provides a stable reference for genome annotation, gene identification and comparative analyses
NCBI Gene https://www.ncbi.nlm.nih.gov/gene DB of genes with information including nomenclature, chromosomal localisation, gene products and more
NCBI Genome https://www.ncbi.nlm.nih.gov/genome Sequence and map data from whole genomes
NCBI protein DB https://www.ncbi.nlm.nih.gov/protein Protein sequence records from a variety of sources including GenPept, RefSeq, Swiss-Prot, PIR, PRF, and PDB
NCBI TSA https://www.ncbi.nlm.nih.gov/Traces/wgs/?view=TSA DB of computationally assembled transcript sequences from primary data such as ESTs and RNA-Seq technologies
Ensembl https://www.ensembl.org/ Genome browser for vertebrate genomes with tools for comparative analysis and predictions
Ensembl Metazoa http://metazoa.ensembl.org/index.html Gene and genome data for Metazoan species
Ensembl Genome http://ensemblgenomes.org Genome data for non-vertebrate species with tools for manipulation, analysis and visualisation
GenomeArk https://www.genomeark.org DB of genome sequencing and assembly data generated by the Earth BioGenome Project, the Vertebrate Genomes Project, the Telomere-to-Telomere Consortium, and other related projects.
PeptideAtlas https://peptideatlas.org Multiorganism compendium of peptides identified from mass spectrometry data
Kalium DB https://kaliumdb.org DB of polypeptidic ligands of potassium channels
ScrepYard https://screpyard.org DB of secreted cysteine-rich repeat peptides
Sequence submission
UniProtKB submissions and updates https://www.uniprot.org/help/submissions UniProt submission and updates portal, linked to protein sequences
NCBI submission portal https://submit.ncbi.nlm.nih.gov NCBI submission and updates portal, linked to nucleotide sequences
DDBJ Nucleotide Sequence Submission https://www.ddbj.nig.ac.jp/ddbj/submission-e.html DDBJ submission and updates portal, linked to nucleotide sequences
ENA Submitting and updating data https://www.ebi.ac.uk/ena/browser/submit ENA submission and updates portal, linked to nucleotide sequences
3D structure, peptide prediction and molecular docking
RCSB-PDB https://www.rcsb.org Archive of 3D structure data for large biological molecules in USA (Research Collaboratory for Structural Bioinformatics-PDB)
PDBe https://www.ebi.ac.uk/pdbe/ Archive of 3D structure data for large biological molecules in Europe (EMBL-EBI)
PDBj https://pdbj.org/ Archive of 3D structure data for large biological molecules in Japan
PDBsum http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl Structural summaries of PDB entries
BMRB https://bmrb.io Archive spectral and quantitative data derived from nuclear magnetic resonance
EMDB (Electron Microscopy Data Bank https://www.ebi.ac.uk/emdb/ Repository of 3D density maps obtained by cryo-electron microscopy (cryo-EM) for macromolecular complexes and subcellular structures
AlphaFold Protein Structure DB https://alphafold.ebi.ac.uk DB of protein structure predictions based on an AI system developed by GoogleDeepMind
AlphaFold2 https://colab.research.google.com/github/sokrypton/ColabFold/blob/main/AlphaFold2.ipynb Server for the prediction of 3D structure from amino acid sequences
AlphaFold3 https://alphafoldserver.com/welcome Server for the prediction of 3D structure from proteins, DNA, RNA with ligands and ions.
AlphaFold Server https://alphafoldserver.com/welcome Web service, powered by AlphaFold 3, that can predict structures containing proteins, DNA, RNA, ligands, ions, and also model chemical modifications for proteins and nucleic acids
SWISS-MODEL repository (SMR) https://swissmodel.expasy.org/ Automated protein structure homology-modeling server
RoseTTAFold https://robetta.bakerlab.org/ Protein structure and interaction prediction server including RoseTTAFold and TrRosetta
SwissDock http://www.swissdock.ch Web service that predicts molecular interactions between a target protein and a small molecule
ClusPro https://cluspro.bu.edu/home.php Web service for protein?protein docking
PeSTo (Protein Structure Transformer https://pesto.epfl.ch/ Web service for predicting protein interaction interfaces with other proteins, nucleic acids, lipids, small molecules, and ions from a protein structure
HADDOCK (High Ambiguity Driven protein-protein DOCKing) https://rascar.science.uu.nl/haddock2.4/ Web service for information-driven flexible docking used to model biomolecular complexes
KNOTTIN https://www.dsimb.inserm.fr/KNOTTIN/index.php DB and prediction tools of small disulfide-rich proteins characterised by cysteine knots
Peptide Ranker http://distilldeep.ucd.ie/PeptideRanker/ Server for the prediction of bioactive peptides based on a neural network
PEP-FOLD3 https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/ Tool for prediction of peptide structure from amino acid sequences
PEP-FOLD4 http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD4 Improved version of PEP-FOLD3 that considers pH and ionic strength variation
Gene function, interactions and networks
Gene ontology (GO) knowledgebase http://geneontology.org/ Human- and machine-readable source of information on the functions of genes
STRING https://string-db.org/ DB of protein associations, including both physical interactions and functional associations
KEGG https://www.genome.jp/kegg/ DB for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from genomic and molecular-level information
IntAct https://www.ebi.ac.uk/intact/home DB and analysis tools for molecular interaction data
Bgee https://www.bgee.org DB for retrieval and comparison of gene expression patterns across animal species
DDBJ GEA https://www.ddbj.nig.ac.jp/gea/ Gene expression repository from array- and sequencing-based data
NCBI GEO https://www.ncbi.nlm.nih.gov/geo/ Gene expression repository from array- and sequencing-based data
ENA ArrayExpress https://www.ebi.ac.uk/biostudies/arrayexpress Gene expression repository from array- and sequencing-based data
Pannzer2 http://ekhidna2.biocenter.helsinki.fi/sanspanz/ Fully automated service for functional annotation of proteins of unknown function
Philius https://www.yeastrc.org/philius/pages/philius/runPhilius.jsp Transmembrane prediction server
SignalP https://services.healthtech.dtu.dk/services/SignalP-6.0/ Prediction of signal peptides and their cleavage sites from amino acid sequences
Phobius https://phobius.sbc.su.se Combined transmembrane topology and signal peptide predictor tool
WoLF PSORT https://wolfpsort.hgc.jp Protein subcellular localisation prediction
The Eukaryotic Linear Motif resource http://elm.eu.org/ Resource for annotation and detection of Eukaryotic Linear Motifs (ELM) or Short Linear Motifs (SLiMs) of adjacent amino acids
WashU Epigenome Browser https://epigenomegateway.wustl.edu/browser/ Genomics data exploration tool for the visualisation, integration and analysis of epigenomic datasets
Gene families and classification
Gene ontology (GO) knowledgebase http://geneontology.org/ Human- and machine-readable source of information on the functions of genes
Blast2GO https://www.biobam.com/blast2go/ Tool for functional annotation using BLAST and Gene Ontology
Pfam http://pfam.xfam.org/ Protein families DB containing multiple sequence alignments and hidden Markov models (HMMs). AVAILABLE. NO LONGER UPDATED
Interpro http://www.ebi.ac.uk/interpro/ Resource providing functional analysis of proteins by classifying them into families and predicting domains and important sites
CATH-Gene3D https://www.cathdb.info/ DB of protein domains classified by structure and evolutionary relationships (Class, Architecture, Topology, and Homology-Gene3D)
PANTHER https://www.pantherdb.org Comprehensive information about the evolution of protein-coding gene families (Protein ANalysis THrough Evolutionary Relationships)
SMART http://smart.embl-heidelberg.de/ Web resource for identification, annotation, and analysis of protein domains and architectures using curated domain models with evolutionary and functional context (Simple Modular Architecture Research Tool)
SUPERFAMILY http://supfam.org/SUPERFAMILY/ DB of structural and functional annotation for all proteins and genomes
The HMMER web server https://www.ebi.ac.uk/Tools/hmmer/home Tool using hidden Markov models for homology search and protein function analysis from sequence data
Quest for Orthologs https://questfororthologs.org/orthology_databases List of orthology databases
OrthoDB https://www.orthodb.org Hierarchical catalog of orthologs - mapping genomics to functional data
OMA https://omabrowser.org/oma/home/ DB and method for the inference of orthologs among complete genomes
NCBI COG https://www.ncbi.nlm.nih.gov/research/cog DB of clusters of orthologous genes
PhylomeDB http://phylomedb.org DB of catalogues of gene phylogenies with phylogenetic trees, orthology predictions and multi-sequence alignments
BLAST https://blast.ncbi.nlm.nih.gov/Blast.cgi Basic Local Alignment Search Tool which finds regions of similarity between nucleotide or amino acid sequences
PROSITE https://prosite.expasy.org DB of protein domains, families and functional sites
NCBI CDD https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml Collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins (conserved domain DB)
Metabolites, lipids, and small molecules
MetaNetX https://www.metanetx.org/ Resource unifying metabolites and biochemical reactions between 12 different resources
MetaboLights https://www.ebi.ac.uk/metabolights/ DB for metabolomics experiments and derived information
HMDB https://hmdb.ca/ DB of small metabolites found in the human body
KEGG COMPOUND https://www.genome.jp/kegg/compound/ DB of small molecules, biopolymers, and other chemical substances relevant to biological systems, linked to pathways, reactions, and disease networks
ChEBI https://www.ebi.ac.uk/chebi/ Dictionary of molecular entities focused on 'small' chemical compounds (Chemical Entities of Biological Interest)
MetaCyc https://metacyc.org/ DB of metabolites, reactions, pathways, enzymes, and genes from all domains of life
NCBI PubChem https://pubchem.ncbi.nlm.nih.gov DB containing chemical information on a variety of compounds
SwissLipids https://www.swisslipids.org/ DB of lipids and their biology
LIPID MAPS https://www.lipidmaps.org/ Lipid portal providing standardized lipid classification, DBs, and tools to support lipidomics research. Enables lipid identification and analysis from biological samples (LIPID Metabolites And Pathways Strategy)
ChemDB http://cdb.ics.uci.edu/ Chemical DB of small molecules with information such as 3D structure, physicochemical properties, and many tools
PTM / glycosylation
iPTMnet https://research.bioinformatics.udel.edu/iptmnet/ PTM resource integrating data mining, literature, and bioinformatics tools
GlyCosmos https://glycosmos.org/ Glycoscience portal integrating glycan, glycomics, and glycoconjugate data, with access to related genes, proteins, lipids, pathways, diseases, and glycomes
glyco@Expasy https://www.expasy.org/resources/glyco-expasy Glycoscience portal centralizing glycoinformatics resources and web tools in glycobiology and glycoproteomics
Enzymes and biochemical reactions
ENZYME https://enzyme.expasy.org/ Repository of information relative to the nomenclature of enzymes
Rhea https://www.rhea-db.org DB for chemical and transport reactions that uses the chemical dictionary
KEGG REACTION https://www.genome.jp/kegg/reaction/ DB of chemical reactions
KEGG PATHWAY https://www.genome.jp/kegg/pathway.html Collection of manually drawn pathway maps representing our knowledge of the molecular interaction, reaction and relation networks
MetaCyc https://metacyc.org/ DB of metabolites, reactions, pathways, enzymes, and genes from all domains of life
BRENDA https://www.brenda-enzymes.org/ DB of functional, biochemical, and molecular biological information on enzymes, including reactions, substrates, and kinetics (BRaunschweig ENzyme DAtabase)
Pharmacology and drugs
IUPHAR https://www.guidetopharmacology.org/ Resource of pharmacological targets and substances that act on them
ChEMBL https://www.ebi.ac.uk/chembl/ Large-scale DB of bioactive, drug-like molecules integrating chemical, bioactivity, and genomic data to support drug discovery and medicinal research
DrugBank https://go.drugbank.com/ Comprehensive drug and drug-target DB integrating chemical, pharmacological, and clinical data to support drug discovery, research, development, and healthcare software integration
Taxonomy
Catalog of Life https://www.catalogueoflife.org/ Catalog of the world's species
GBIF https://www.gbif.org/ Catalog of data about all types of life on Earth
European Scorpion database https://www.ntnu.no/ub/scorpion-files Catalog of European scorpion
The Reptile Database http://reptile-database.org Catalog of reptiles
SnakeDB http://snakedb.org/ Catalog of snakes and relative venom toxicity (LD(50)
Spiders of Europe https://araneae.nmbe.ch Catalog of European spiders
World Spider Catalog https://wsc.nmbe.ch Catalog of world spiders
Repfocus http://www.repfocus.dk Catalog of reptiles
Snakebd http://www.snakebd.com/ Catalog of indigenous snake species of Bangladesh with respective venom composition
WoRMS https://www.marinespecies.org Authoritative classification and catalogue of marine species
NCBI Taxonomy https://www.ncbi.nlm.nih.gov/taxonomy/ Primary DB for taxonomy of any organism
UniProt Taxonomy https://www.uniprot.org/taxonomy UniProt taxonomy
Antimicrobial peptides
APD3 https://aps.unmc.edu Antimicrobial peptide DB
DRAMP http://dramp.cpu-bioinfor.org Data Repository of Antimicrobial Peptides harboring annotations including patents and clinical trials and therapeutic applications (Data Repository of AntiMicrobial Peptides)
DBAASP https://dbaasp.org/home Database of Antimicrobial Activity and Structure of Peptides providing information and analytical resources for designing antimicrobial compounds with a high therapeutic index
CAMPR3 http://www.camp3.bicnirrh.res.in Collection of anti-microbial peptides containing information related to sequence, protein definition, accession numbers, activity, source organism, target organisms and more.
LAMP2 http://biotechlab.fudan.edu.cn/database/lamp/ Resource and tools for antimicrobial peptide studies CURRENTLY UNAVAILABLE
Anticancer peptides and proteins
canSAR https://cansar.ai Portal for multidisciplinary data search and AI predictions useful for drug discovery
PaccMann https://huggingface.co/spaces/jannisborn/paccmann Web service for anticancer compound sensitivity prediction
Evicor https://www.evicor.org Web platform for exploration of molecular features and response to anti-cancer drugs
ApInAPDB http://bioinf.modares.ac.ir/software/ApInAPDB/ Apoptosis-inducing anticancer peptides database CURRENTLY UNAVAILABLE
CancerPPD http://crdd.osdd.net/raghava/cancerppd/ DB of experimentally verified anticancer peptides and proteins AVAILABLE BUT NOT UPDATED SINCE 2015
Human disease resources
DISGENET https://disgenet.com/ Gene-disease association network
OMIM https://www.omim.org/ Catalog of human genes and genetic disorders
Orphanet https://www.orpha.net/ Knowledge on rare diseases and orphan drugs
ClinPGx https://www.clinpgx.org/ Clinical pharmacogenomic (PGx) resource
Morphology
Uberon http://obophenotype.github.io/uberon/ Integrated cross-species anatomy ontology
Morphobank https://morphobank.org/ Homology of phenotypes over the web and a DB of peer-reviewed morphological matrices
Model organisms
SIMRbase https://simrbase.stowers.org Genome Browser for various species including the sea anemone Nematostella vectensis and the worm anemone Scolanthus callimorphus
Hydra 2.0 Web portal https://research.nhgri.nih.gov/hydra/ Genome Browser and data search for Hydra vulgaris
Flybase https://flybase.org/ DB of Drosophila genes and genomes
Human protein Atlas https://www.proteinatlas.org/ Resource for exploration of the human proteome
Mouse Genome Informatics https://www.informatics.jax.org/ DB for the laboratory mouse, providing integrated genetic, genomic, and biological data
Mousephenotype https://www.mousephenotype.org Resource for mouse gene function
Rat Genome Database https://rgd.mcw.edu/ DB for genetic, genomic, phenotype, and disease-related data generated from rat research
Zebrafish https://zfin.org DB of genetic and genomic data for the zebrafish (Danio rerio) as a model organism
MolluscDB http://mgbase.qnlm.ac Integrated genomics DB for Mollusca
World Spider Trait database https://spidertraits.sci.muni.cz DB of morphological, ecological and other biological traits of spiders
GeneCards https://www.genecards.org Human Gene DB providing comprehensive information on all annotated and predicted human genes
Galleria mellonella https://www.gmrcuk.org/ The UK Hub for Galleria mellonella Research and Resources
Cell line resources
Cellosaurus https://www.cellosaurus.org/ A knowledge resource on cell lines used in biomedical research
Recombinant expression
Addgene https://www.addgene.org/ Repository of plasmids and antibodies
Resource portals
NCBI https://www.ncbi.nlm.nih.gov Comprehensive resource portal for biomedical and genomic data and tools from the National Library of Medicine
Expasy https://www.expasy.org/ Bioinformatics resource portal of the Swiss Institute of Bioinformatics (SIB) providing access to over 160 databases and software tools for a range of life science domains.
Galaxy https://usegalaxy.org Web-based platform for genomics data including hundreds of tools
EMBL-EBI services https://www.ebi.ac.uk/services Molecular data resources and analysis tools maintained by the European Bioinformatics Institute (EMBL-EBI)
Database Commons https://ngdc.cncb.ac.cn/databasecommons/ Catalog of worldwide biological DBs
Ontobee https://ontobee.org Linked data server to facilitate ontology data sharing, visualization, query, integration, and analysis
OLS https://www.ebi.ac.uk/ols4/ Repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions
BioPortal https://bioportal.bioontology.org Repository of biomedical ontologies
Clinical and public health toxinology
Toxbase https://www.toxbase.org/ Subscription-based clinical toxicology DB of the UK National Poisons Information Service
Merative Micromedex https://www.micromedexsolutions.com/home/dispatch/ssl/true Subscription-based resource for healthcare professionals including toxicology information
Munich AntiVenom Index (MAVIN) https://www.antivenoms.toxinfo.med.tum.de List of antivenom holding centers, venomous animals, and antivenoms. LAST UPDATE 2016
Clinical Toxinology Resources http://www.toxinology.com Repository of information on venomous and poisonous animals, plants and mushrooms.
AfriTox https://www.afritox.co.za Subscription-based poisons information focused on Africa
Merative Micromedex https://www.micromedexsolutions.com/home/dispatch Subscription-based clinical resources for healthcare professionals
Toxinz https://www.toxinz.com Subscription-based resource of evidence-based information for the clinical management of poisoned patients
The AntiBodies Chemically Defined (ABCD) Database https://web.expasy.org/abcd/ Repository of sequenced antibodies, integrating curated information about the antibody and its antigen with cross-links to standardized DB of chemical and protein entities
Clinical research platform https://clinicaltrials.gov/ DB of clinical study registrations, protocols, participant criteria, interventions, locations, results summaries, adverse events, and links to related health information and publications
WHO Snakebite https://www.who.int/teams/control-of-neglected-tropical-diseases/snakebite-envenoming/snakebite-information-and-data-platform WHO snakebite information and data platform
WHO Antivenom https://www.who.int/teams/control-of-neglected-tropical-diseases/snakebite-envenoming/antivenoms WHO snakebite antivenom guidelines
Patent search tools and documentation
Espacenet from the European Patent Office (EPO) https://worldwide.espacenet.com/ Patent search tool from the European Patent Office (EPO), offering access to over 100 million patent documents from more than 100 countries
Patentscope from the World Intellectual Property Organization (WIPO) https://patentscope.wipo.int Patent search tool from the World Intellectual Property Organization (WIPO) offering access to over 80 million international and national patent documents
International organisations
WHO https://www.who.int World Health Organisation with a section specific to snakebites and antivenoms
IUCN https://www.iucn.org Global authority on the status of the natural world and the measures needed to safeguard it
WAHIS https://wahis.oie.int Global animal health reference DB of the World Organisation for Animal Health (WOAH)
IST https://www.toxinology.org The International Society of Toxinology
SFT https://www.sftox.com French Society of Toxinology
EAPCCT https://www.eapcct.org European Association of Poisons Control and Clinical Toxicology
AACT https://www.clintox.org American Academy of Clinical Toxicology