TABLE 1.
List of peptide sequences and databases containing their structures.
| Database | Peptide type | URL | References | |
| Antimicrobial peptides (AMPs) database | ||||
| Peptaibol | Peptaibol | Sequence and structure resource for the unusual class of peptides known as peptaibols | http://www.cryst.bbk.ac.uk/peptaibol | Whitmore and Wallace, 2004 |
| Defensins Knowledgebase | Defensins | A manually curated database of more than 350 defensin records each containing sequence, structure and activity information | http://defensins.bii.a-star.edu.sg | Seebah et al., 2007 |
| PhytAMP | Plant AMPs | A specialized database for plant AMPs containing sequence information and physicochemical or biological data, along with a set of tools for sequence analysis | http://phytamp.hammamilab.org/ | Hammami et al., 2009 |
| BACTIBASE | Bacteriocins | A manually curated database of bacterial antimicrobial peptides, along with various tools for bacteriocin analysis, such as homology search, multiple sequence alignments, Hidden Markov Models, molecular modeling | http://bactibase.hammamilab.org/main.php | Hammami et al., 2010 |
| BaAMPs | AMP | A manually curated database of AMPs specifically assayed against microbial biofilms | http://www.baamps.it | Di Luca et al., 2015 |
| APD3 | AMP | A AMPs database including a total of 2619 peptides, which currently focuses on natural AMPs with defined sequences and activities and also provides other searchable annotations, including target pathogens, molecule-binding partners, post-translational modifications and animal models. | https://wangapd3.com/main.php | Wang et al., 2016 |
| CAMPR3 | AMP | A database of sequences, structures and family-specific signatures of prokaryotic and eukaryotic AMPs containing 10247 sequences, 757 structures and 114 family-specific signatures | www.camp3.bi cnirrh.res.in. | Waghu et al., 2016 |
| InverPep | Invertebrates AMPs | A manually curated database specialized in experimentally validated AMPs from invertebrates and its information | ciencias.medellin. unal.edu.co/gruposde investigacion/prospeccionydisenobiomoleculas/InverPep/public/home_en | Gómez et al., 2017 |
| MBPDB | Milk bioactive peptide | A comprehensive database of bioactive peptides derived from milk proteins from any mammalian source | http://mbpdb.nws.oregonstate.edu | Nielsen et al., 2017 |
| BAGEL4 | Bacteriocins | A mining web server of RiPPs (ribosomally synthesized and posttranslationally modified peptides) and bacteriocins | http://bagel4.molgenrug.nl | van Heel et al., 2018 |
| DBAASP v3 | AMP | A continuously updated database of antimicrobial activity and structure of peptides | http://dbaasp.org. | Pirtskhalava et al., 2021 |
| Targeted delivery-related databases | ||||
| TumorHope | Therapeutic Peptides | A database of experimentally validated tumor homing peptides containing 744 peptides with information on sequence, target tumor, target cell, peptide receptor, techniques of identification, and also providing secondary/tertiary structure, amino acid composition, and physicochemical properties of peptides which derived from their sequences | http://crdd.osdd.net/raghava/tumorhope/. | Kapoor et al., 2012 |
| CPPsite 2.0 | Cell penetrating peptide | A manually curated database of cell-penetrating peptides containing around 1850 peptide entries and providing predicted tertiary structure of peptides, possessing both modified and natural residues | http://crdd.osdd.net/raghava/cppsite/ | Agrawal et al., 2016 |
| Disease-specific databases | ||||
| Hemolytik | Hemolytic and non-hemolytic peptides | A manually curated resource of experimentally determined hemolytic and non-hemolytic peptides containing 3000 entries that include ∼2000 unique peptides with information on sequence, name, origin, reported function, property such as chirality, types (linear and cyclic), end modifications as well as providing predicted tertiary structure of each peptide | http://crdd.osdd.net/raghava/hemolytik/ | Gautam et al., 2014 |
| AVPdb | Antiviral peptides | A resource of experimentally verified antiviral peptides targeting over 60 medically important viruses including Influenza, HCV, HSV, RSV, HBV, DENV, SARS, etc. containing detailed information of 2683 peptides, including 624 modified peptides experimentally tested for antiviral activity | http://crdd.osdd.net/servers/avpdb/ | Qureshi et al., 2014 |
| ParaPep | Antiparasitic peptides | A repository of experimentally validated antiparasitic peptide sequences and their structures | http://webs.iiitd.edu.in/raghava/parapep/ | Mehta et al., 2014 |
| CancerPPD | Anticancer peptides | A manually curated resource of experimentally verified anticancer peptides (ACPs) and anticancer proteins, consists of 3491 ACP and 121 anticancer protein entries, and contains peptides having non-natural, chemically modified residues and D-amino acids | http://crdd.osdd.net/raghava/cancerppd/ | Tyagi et al., 2015 |
| SATPdb | Bioactive peptide | A database of structurally annotated therapeutic peptides, holds 19192 unique experimentally validated therapeutic peptide sequences having length between 2 and 50 amino acids, and covers peptides having natural, non-natural, and modified residues | http://crdd.osdd.net/raghava/satpdb/ | Singh et al., 2016 |
| THPdb | FDA- approved therapeutic peptides | A manually curated resource of FDA-approved therapeutic peptides and proteins with information on their sequences, chemical properties, composition, disease area, mode of activity, physical appearance, category or pharmacological class, pharmacodynamics, route of administration, toxicity, and target of activity | http://crdd.osdd.net/raghava/thpdb/ | Usmani et al., 2017 |
| StraPep | Bioactive peptide | Collection of all the bioactive peptides with known structure, containing 3791 bioactive peptide structures, which belong to 1312 unique bioactive peptide sequences | http://isyslab.info/StraPep | Wang et al., 2018 |
| BIOPEP-UWM | Bioactive peptide | A continuously updated database of bioactive peptides derived from foods | http://www.uwm.edu.pl/biochemia | Minkiewicz et al., 2019 |
| WALTZ-DB 2.0 | Amyloid-forming peptide | A database providing information on experimentally determined amyloid-forming hexapeptide sequences | http://waltzdb.switchlab.org/ | Louros et al., 2020 |
| Special peptides databases | ||||
| NeuroPedia | Neuropeptides | A Neuropeptide Database, provided through hyperlinks to bioinformatic databases on genome and transcripts, protein structure and brain expression of Neuropeptides | www.neuropeptides.nl | Burbach, 2010 |
| NeuroPedia | Neuropeptides | A neuropeptide databank of peptide sequences (including genomic and taxonomic information) and spectral libraries of identified MS/MS spectra of homolog neuropeptides from multiple species | http://proteomics.ucsd.edu/Software/NeuroPedia/ | Kim et al., 2011 |
| ConoServer | (Venom toxin peptide) conopeptides | A specialized database of sequence and structures of conopeptides (expressed in carnivorous marine cone snails) | http://www.conoserver.org | Kaas et al., 2012 |
| DADP | Anuran defense peptides | A manually curated resource of anuran defense peptides containing 2571 entries with a total of 1923 non-identical bioactive sequences | http://split4.pmfst.hr/dadp/ | Novković et al., 2012 |
| Quorumpeps? | Quorum sensing peptides | A database of quorum sensing peptides with information on structure, activity, physicochemical properties, and related literature | http://quorumpeps.ugent.be/ | Wynendaele et al., 2013 |
| NeuroPep | Neuropeptides | A comprehensive and most complete resource of neuropeptides, which holds 5949 non-redundant neuropeptides together with information on source organisms, tissue specificity, families, names, post-translational modifications, 3D structures (if available) and literature references | http://isyslab.info/NeuroPep | Wang et al., 2015 |
| ArachnoServer 3.0 | (Venom toxin peptide) (Spider venom) | A manually collection of information on the sequence, structure, function and pharmacology of spider-venom toxin peptides | http://arachnoserver.org/ | Pineda et al., 2018 |
| Norin | Non-ribosomal peptides | A database of non-ribosomal peptides together with tools for their analysis containing 1740 peptides | https://bioinfo.cristal.univ-lille.fr/norine/ | Flissi et al., 2020 |