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Peptide Databases & Research Resources

Whether you're a graduate student running a literature search, a clinician checking the evidence behind a peptide therapy, or a curious reader trying to verify claims from a supplement company, knowing where to find reliable peptide data is half the battle.

Whether you're a graduate student running a literature search, a clinician checking the evidence behind a peptide therapy, or a curious reader trying to verify claims from a supplement company, knowing where to find reliable peptide data is half the battle. The information exists --- scattered across dozens of databases, journals, and registries.

This guide maps the territory. We cover the major peptide sequence databases, structural repositories, clinical trial registries, literature search tools, and free full-text resources. Think of it as a research toolkit for anyone who wants to go beyond surface-level peptide information.

Table of Contents

General Protein and Peptide Databases

These are the foundational resources that underpin most peptide research. They cover broad categories of proteins and peptides across all organisms.

UniProt (Universal Protein Knowledgebase)

URL: uniprot.org

UniProt is the single most comprehensive protein database in existence. It combines data from Swiss-Prot (manually curated, high-quality entries), TrEMBL (automatically annotated), and PIR (protein information resource). The 2025 release contains over 250 million protein sequences.

What you'll find: Amino acid sequences, protein function, post-translational modifications, subcellular localization, disease associations, cross-references to other databases, literature citations.

Best for: Looking up any specific peptide hormone, signaling peptide, or therapeutic peptide's sequence and known biology. Start here when you need a reliable reference sequence.

Tip: Use the advanced search to filter by peptide length (e.g., 5-50 amino acids) and organism (Homo sapiens) to narrow results to human peptides specifically.

NCBI Protein Database

URL: ncbi.nlm.nih.gov/protein

Maintained by the National Center for Biotechnology Information, this database integrates protein sequences from GenBank, RefSeq, Swiss-Prot, PDB, and other sources. It's tightly linked to PubMed, Gene, and other NCBI tools.

Best for: Cross-referencing peptide sequences with genetic information, finding protein variants, and linking to published research.

Specialized Peptide Databases

These databases focus specifically on peptides rather than proteins at large. Each one serves a different research niche.

APD (Antimicrobial Peptide Database)

URL: aps.unmc.edu

The APD is the original antimicrobial peptide database, first launched in 2003 by Guangshun Wang at the University of Nebraska Medical Center. As of January 2026, the latest version --- APD6 --- contains 6,309 peptides: 3,379 natural antimicrobial peptides (AMPs), 2,290 synthetic AMPs, and 373 AI-predicted AMPs. Natural AMPs span all six kingdoms of life, from 430 bacterial bacteriocins to 2,628 animal-derived peptides.

What you'll find: Peptide sequences, source organisms, antimicrobial activities, 3D structures (where available), and the AMP Information Pipeline (AMPIP) for systematic data analysis.

Best for: Anyone researching antimicrobial peptides or LL-37 and related defense molecules. The APD's search tools let you filter by activity spectrum (anti-Gram-positive, anti-Gram-negative, antifungal, antiviral).

SATPdb (Structurally Annotated Therapeutic Peptides)

URL: crdd.osdd.net/raghava/satpdb

SATPdb aggregates data from 22 public peptide databases into a single platform. It holds 19,192 unique experimentally validated therapeutic peptide sequences (2 to 50 amino acids), organized into 10 functional categories: anticancer (1,099), antimicrobial (10,585), drug delivery (1,642), antihypertensive (1,698), and others.

What you'll find: Peptide sequences, 3D structures (assigned via PDB or predicted using I-TASSER and PEPstrMOD), therapeutic classifications, physicochemical properties.

Best for: Finding peptides with specific therapeutic activities. The database's strength is its structural annotation --- you can search for peptides with particular 3D conformations alongside their biological activities.

BIOPEP-UWM

URL: uwm.edu.pl/biochemia/index.php/en/biopep

BIOPEP specializes in bioactive peptides derived from food proteins --- the kind released during digestion or fermentation. Think of ACE-inhibitory peptides from milk casein, antioxidant peptides from soy, or bitter peptides in cheese.

What you'll find: Peptide sequences, source proteins, bioactivities (antihypertensive, antioxidant, antimicrobial, opioid-like, immunomodulatory), enzyme cleavage predictions, SMILES codes for computational chemistry.

Best for: Food science researchers, nutraceutical development, and anyone investigating the bioactive peptides released when dietary proteins are digested.

DRAMP 4.0 (Data Repository of Antimicrobial Peptides)

URL: dramp.cpu-bioinfor.org

DRAMP focuses on antimicrobial peptide data relevant to clinical translation. The 2025 update contains entries on natural, synthetic, and patented AMPs, with emphasis on activity data, minimum inhibitory concentrations (MICs), and structure-activity relationships.

Best for: Researchers working on translating AMPs from bench to bedside, especially those needing quantitative activity data.

THPdb2 (Therapeutic Peptides Database)

URL: Published in Drug Discovery Today, 2024

THPdb2 is a curated database of FDA-approved therapeutic peptides and proteins. It contains 6,385 entries covering 894 FDA-approved therapeutics, including 85 peptides/polypeptides and 354 monoclonal antibodies. Each entry includes drug name, target, mechanism, indication, approval year, and regulatory status.

Best for: Quickly checking whether a specific peptide has FDA approval and finding its approved indications.

CPPsite 2.0

URL: webs.iiitd.edu.in/raghava/cppsite

The dedicated database for cell-penetrating peptides. Contains over 1,800 experimentally validated CPP sequences with uptake efficiency data, cargo information, and cell line specificity.

Best for: Researchers designing peptide-based drug delivery systems who need to compare CPP properties and select candidates for their specific cargo and target cell type.

Structural Databases

Understanding a peptide's 3D structure is often essential for understanding how it works.

RCSB Protein Data Bank (PDB)

URL: rcsb.org

The PDB is the global archive for experimentally determined 3D structures of biological macromolecules. Structures are solved by X-ray crystallography, NMR spectroscopy, or cryo-electron microscopy. As of 2026, it holds over 220,000 structures.

What you'll find: 3D coordinates for peptides and proteins, ligand-binding information, visualization tools, validation reports.

Best for: Examining how a peptide folds, how it binds to its receptor, or how a drug analog differs structurally from the natural peptide. Use the built-in 3D viewer (Mol*) to rotate and inspect structures without downloading software.

Peptide-specific tip: Search for short peptides by filtering for entries with fewer than 50 residues. Many peptide hormone structures are co-crystallized with their receptors, giving you the binding interface.

AlphaFold Protein Structure Database

URL: alphafold.ebi.ac.uk

DeepMind's AlphaFold has predicted structures for over 200 million proteins. While its predictions are most reliable for well-folded globular proteins (and less so for short, flexible peptides), it provides useful starting structures for peptide hormone precursors and receptors.

Best for: Getting a structural model when no experimental PDB structure exists.

Literature Search Tools

PubMed

URL: pubmed.ncbi.nlm.nih.gov

PubMed indexes over 37 million citations from biomedical journals worldwide. It is free, maintained by the U.S. National Library of Medicine, and is the standard starting point for any biomedical literature search.

Key features for peptide researchers:

  • MeSH terms: Use Medical Subject Headings for precise searches. "Peptide Hormones" [MeSH] will capture all articles indexed under that heading, even if the exact phrase doesn't appear in the title or abstract
  • Boolean operators: Combine terms with AND, OR, NOT to refine results
  • Filters: Limit by publication date, article type (review, clinical trial, meta-analysis), species (human only), and free full-text availability
  • Single Citation Matcher: Find a specific article when you have only partial citation details (author, journal, year, partial title)

Google Scholar

URL: scholar.google.com

Broader than PubMed --- it indexes books, theses, conference papers, and preprints alongside journal articles. The "Cited by" feature helps you trace how a seminal peptide paper influenced subsequent research.

Tip: Install Google Scholar Button (browser extension) to check if free full-text versions exist when you hit a paywall.

Scopus and Web of Science

Subscription-based databases offering citation analysis, journal rankings, and more sophisticated search filters than PubMed. Available through most university libraries. Useful for systematic reviews where comprehensive coverage matters.

Clinical Trial Registries

If you want to know whether a peptide has been tested in humans --- and what the results were --- clinical trial registries are essential.

ClinicalTrials.gov

URL: clinicaltrials.gov

Run by the U.S. National Library of Medicine, ClinicalTrials.gov is the world's largest clinical trial registry. It lists over 490,000 studies from 230 countries.

Peptide-specific data: A 2025 analysis found 1,399 clinical trials specifically involving peptide therapeutics, testing 273 distinct peptides. Over 200 trials for peptide vaccines alone were registered between 2023 and 2024. Another search found more than 350 interventional peptide vaccine studies (Phases I-IV).

How to search effectively:

  1. Go to clinicaltrials.gov/search
  2. Enter the peptide name (e.g., "semaglutide" or "BPC-157") in the search bar
  3. Use the "Intervention/treatment" field for more precise results
  4. Filter by study phase (Phase 1, 2, 3, 4), recruitment status (recruiting, completed), and study type (interventional vs. observational)
  5. Check "Has Results" to find completed trials that have posted their outcome data

What to look for: The "Results" tab on completed trials shows primary and secondary endpoints, adverse events, and statistical analyses. Not all trials post results, but an increasing number do under legal requirements.

WHO International Clinical Trials Registry Platform (ICTRP)

URL: trialsearch.who.int

The WHO ICTRP aggregates trial registrations from ClinicalTrials.gov, the EU Clinical Trials Register, ISRCTN, and national registries from Japan, China, India, and other countries. Use it to find trials that might not be listed on ClinicalTrials.gov.

EU Clinical Trials Register

URL: clinicaltrialsregister.eu

For trials conducted in the European Union. Useful for finding peptide studies by European pharmaceutical companies that may not be registered on ClinicalTrials.gov.

Free Full-Text Resources

Hitting a paywall when you find the perfect paper is frustrating. These resources help.

PubMed Central (PMC)

URL: ncbi.nlm.nih.gov/pmc

PMC is the free full-text archive of biomedical and life sciences journal literature at the NIH. Over 9 million articles are available. When searching PubMed, look for the "Free PMC article" label --- clicking it takes you directly to the full text.

Pro tip: On PubMed, filter your search results by "Free full text" on the left sidebar to show only open-access articles.

Unpaywall

URL: unpaywall.org

A browser extension that automatically detects free legal versions of paywalled papers. It checks publisher open-access pages, institutional repositories, and PMC. Install it in Chrome or Firefox and a green padlock icon appears on paywalled article pages when a free version exists somewhere online.

  • Your local library: Many public libraries provide access to JSTOR, ScienceDirect, and other databases. Check your library card.
  • Interlibrary loan (ILL): Request any article through your library's ILL service. Typically free and takes 1-3 days.
  • Author requests: Email the corresponding author. Most researchers will happily send a PDF of their paper.
  • Preprint servers: bioRxiv (biorxiv.org) and medRxiv (medrxiv.org) host preprints (pre-peer-review versions) of many peptide research papers.

Computational Peptide Tools

These tools help researchers analyze, predict, and design peptides computationally.

ToolURLFunction
PeptideRankerpeptideranker.silverquill.comPredicts the probability that a peptide is bioactive
Peptide-ToolsOnline web serverCalculates isoelectric points and chemical stability liabilities for natural and modified peptides
PEPstrMODwebs.iiitd.edu.in/raghava/pepstrmodPredicts 3D structures of peptides containing modified residues
SignalP 6.0services.healthtech.dtu.dk/services/SignalP-6.0Predicts signal peptides and cleavage sites
ToxinPredwebs.iiitd.edu.in/raghava/toxinpredPredicts peptide toxicity
AntiCP 2.0webs.iiitd.edu.in/raghava/anticp2Predicts anticancer peptides
CAMPR4camp.bicnirrh.res.inCollection of AMP prediction tools
BLAST (NCBI)blast.ncbi.nlm.nih.govSearches for similar peptide/protein sequences across databases
Peptide Mass CalculatorMultiple sitesCalculates molecular weight, charge, and hydrophobicity from amino acid sequence

Integrated and Emerging Platforms

Peptipedia v2.0

Published in Database (Oxford) in 2024, Peptipedia v2.0 consolidates data from multiple peptide databases --- APD, LAMP, DRAMP, UniProt, SATPdb, and others --- into one searchable platform. Before Peptipedia, finding information across fragmented databases required visiting each one individually. Peptipedia v2.0 aims to solve this integration problem.

Comprehensive Therapeutic Peptide Dataset (2025)

A 2025 paper in Scientific Data (Nature) presented a dataset of 58,583 experimentally validated therapeutic peptides with annotated structure information. It integrates data from function-specific databases (antimicrobial, antiviral, glucose-regulating) alongside comprehensive repositories like SATPdb, EROP-Moscow, and BIOPEP-UWM. The dataset specifically addresses the gap in multifunctional peptide data and structural annotations.

PepBank

Originally developed at Massachusetts General Hospital, PepBank is a searchable archive of peptide sequences and associated biological data. It offers Google-like quick search, advanced field-specific search, and sequence similarity search (BLAST and Smith-Waterman algorithms). While less actively updated than some alternatives, it remains a useful resource for finding peptide sequences mentioned in published literature.

PubMed Search Strategies for Peptide Research

Effective literature searching is a skill. Here are field-tested strategies for common peptide research questions.

Strategy 1: Finding All Research on a Specific Peptide

Search: "BPC-157"[Title/Abstract] OR "BPC 157"[Title/Abstract] OR "body protection compound 157"[Title/Abstract]

Include all common name variants. Peptide naming is inconsistent across the literature --- BPC-157 appears as "BPC-157," "BPC 157," and "body protection compound-15."

When you need to capture everything published on a topic:

("peptide therapeutics"[MeSH] OR "antimicrobial peptides"[MeSH] OR
"peptide drugs"[Title/Abstract]) AND ("clinical trial"[Publication Type]
OR "randomized controlled trial"[Publication Type]) AND "humans"[MeSH Terms]

This limits results to human clinical trials involving peptide drugs.

Strategy 3: Finding Reviews and Overviews

Add AND (review[Publication Type] OR "systematic review"[Publication Type] OR meta-analysis[Publication Type]) to any search to filter for review articles --- a good starting point for understanding the state of evidence.

Strategy 4: Staying Current

Set up a PubMed email alert (My NCBI > Saved Searches) for your peptide of interest. PubMed will email you whenever new papers matching your search are indexed.

FAQ

Which peptide database should I start with?

For general peptide information, start with UniProt. For therapeutic peptides specifically, SATPdb or THPdb2 are more focused. For antimicrobial peptides, the APD is the gold standard. For food-derived bioactive peptides, use BIOPEP-UWM.

How do I find out if a peptide has been tested in clinical trials?

Search ClinicalTrials.gov by the peptide's name. Check the WHO ICTRP for international trials. For FDA-approved peptides, consult FDA's Drugs@FDA database or the Purdue CDEK FDA Approvals database.

Are these databases free to use?

Yes. PubMed, PMC, UniProt, PDB, APD, ClinicalTrials.gov, and most specialized peptide databases are free. Google Scholar is free. Scopus and Web of Science require institutional subscriptions but can often be accessed through public or university libraries.

How often are peptide databases updated?

It varies. UniProt and PDB receive monthly updates. The APD is updated as new AMPs are published (APD6 was released in late 2025). SATPdb receives periodic updates. ClinicalTrials.gov is updated continuously as investigators register new trials and post results.

How can I tell if a peptide study is reliable?

Look for: publication in a peer-reviewed journal, adequate sample size, appropriate controls, clear statistical methods, and disclosure of funding sources and conflicts of interest. For clinical claims, prioritize randomized controlled trials and systematic reviews over case reports and animal studies. Our guide on how to interpret peptide research papers covers this in detail.

What's the difference between PubMed and PubMed Central?

PubMed is a citation index --- it lists articles with titles, abstracts, and metadata but usually links out to journals for full text. PubMed Central (PMC) is the full-text archive where you can read the entire paper for free. Not every PubMed citation has a PMC full-text version.

The Bottom Line

The peptide research ecosystem is rich but fragmented. No single database covers everything. A thorough research effort typically involves checking UniProt for sequence and function data, PDB for structural information, PubMed for published literature, ClinicalTrials.gov for human trial data, and one or more specialized databases (APD, SATPdb, BIOPEP) depending on the specific question.

The good news: almost all of these resources are free. The barrier to accessing peptide research isn't cost --- it's knowing where to look and how to search effectively. Bookmark the databases listed here, learn the PubMed search operators, and set up email alerts for topics you follow regularly. In a field moving as fast as peptide science, staying current is as important as understanding the fundamentals.

For an introduction to peptide biology, start with our beginner's guide to peptides. For help evaluating specific claims, see our guide on how to read peptide research.

References

  1. APD6: the antimicrobial peptide database is expanded to promote research and development by deploying an unprecedented information pipeline. Nucleic Acids Research. 2025. https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf860/8250474

  2. SATPdb: a database of structurally annotated therapeutic peptides. Nucleic Acids Research. 2016;44(D1):D1119-D1126. https://pmc.ncbi.nlm.nih.gov/articles/PMC4702810/

  3. Peptipedia v2.0: a peptide sequence database and user-friendly web platform. Database. 2024. https://academic.oup.com/database/article/doi/10.1093/database/baae113/7887558

  4. A comprehensive dataset of therapeutic peptides on multi-function property and structure information. Scientific Data. 2025. https://www.nature.com/articles/s41597-025-05528-1

  5. THPdb2: compilation of FDA approved therapeutic peptides and proteins. Drug Discovery Today. 2024. https://www.sciencedirect.com/science/article/abs/pii/S1359644624001727

  6. PepBank: a database of peptides based on sequence text mining and public peptide data sources. Nucleic Acids Research. 2008;36(Database issue):D545-D551. https://pmc.ncbi.nlm.nih.gov/articles/PMC1976427/

  7. Peptide Utility (PU) search server: A new tool for peptide sequence search from multiple databases. Heliyon. 2022. https://pmc.ncbi.nlm.nih.gov/articles/PMC9800339/

  8. Advance in peptide-based drug development: delivery platforms, therapeutics and vaccines. Signal Transduction and Targeted Therapy. 2024. https://www.nature.com/articles/s41392-024-02107-5

  9. Advancing peptide-based vaccines against viral pathogens: a narrative review. Annals of Medicine. 2025. https://pmc.ncbi.nlm.nih.gov/articles/PMC12864683/