Everything you need to know about visualizing and analyzing peptide structures in PepDraw
Get started with PepDraw in just a few simple steps:
Type directly into the sequence field or click amino acid buttons using single-letter codes (A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y).
Use the pH slider to see how ionizable amino acids change their protonation states at different pH values.
Watch the chemical structure render in real-time along with calculated properties like mass, pI, charge, and hydrophobicity.
Download free images in PNG or JPG format. Pro feature coming soon: SVG and PDF format for use in scientific publications, presentations, or educational materials.
PepDraw is a powerful yet user-friendly tool designed to facilitate the study of peptide chemical structures and properties. It allows researchers, students, and educators to:
PepDraw is especially useful for teaching students about amino acid structure and properties. The real-time visualization helps bridge the gap between sequence and structure.
Type your peptide sequence directly into the sequence entry field using standard single-letter amino acid codes. PepDraw automatically recognizes and processes the 20 standard amino acids.
Click the buttons in the amino acid palette to build your sequence one residue at a time. This method is great for beginners or when teaching amino acid structures.
PepDraw reads only the 20 standard amino acid codes: A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y. Any other characters will be ignored.
| Code | Amino Acid | Properties |
|---|---|---|
| A | Alanine | Hydrophobic, small |
| C | Cysteine | Polar, can form disulfides |
| D | Aspartic acid | Acidic, negatively charged |
| E | Glutamic acid | Acidic, negatively charged |
| F | Phenylalanine | Aromatic, hydrophobic |
| G | Glycine | Smallest, flexible |
| H | Histidine | Basic, aromatic, pH-sensitive |
| I | Isoleucine | Hydrophobic, branched |
| K | Lysine | Basic, positively charged |
| L | Leucine | Hydrophobic, branched |
| M | Methionine | Hydrophobic, contains sulfur |
| N | Asparagine | Polar, uncharged |
| P | Proline | Cyclic, creates kinks |
| Q | Glutamine | Polar, uncharged |
| R | Arginine | Basic, positively charged |
| S | Serine | Polar, small |
| T | Threonine | Polar, can be phosphorylated |
| V | Valine | Hydrophobic, branched |
| W | Tryptophan | Aromatic, hydrophobic, largest |
| Y | Tyrosine | Aromatic, polar |
PepDraw automatically calculates comprehensive peptide properties as you enter your sequence. All calculations update in real-time.
Critical properties such as net charge vary with pH. Use the pH slider to see how your peptide behaves under different conditions. This is especially important for peptides with histidine, aspartic acid, glutamic acid, lysine, arginine, cysteine, or tyrosine residues.
PepDraw generates professional-quality chemical structures showing the complete peptide backbone and all side chains with proper stereochemistry (line-dash-wedge notation).
Adjusting the pH slider changes the protonation state of ionizable amino acids:
PepDraw supports multiple export formats to suit different use cases:
For the highest quality prints, use SVG format when possible. Vector graphics remain sharp at any resolution, making them perfect for journal submissions and large-format posters.
Have questions, feedback, or need assistance with PepDraw? We're here to help!
Educators: We welcome the use of PepDraw in classroom settings! Let us know if you need any additional features or resources for teaching.
If you use PepDraw in your research, teaching, or publications, please cite it using one of these formats:
Proper citation helps demonstrate PepDraw's impact on the scientific community and supports continued development and maintenance. Over 1000+ researchers use PepDraw weekly, and citations help justify resources dedicated to keeping this tool free and accessible.
Always include the version number (currently 4.0) in your citations. This ensures:
Need help with citation format for a specific journal or style guide? Have questions about methodology to include in your methods section? Contact us at support@pepdraw.com
Currently, PepDraw 4.0 supports the 20 standard amino acids. Support for modified and non-canonical amino acids is planned for future releases.
All calculations use established scientific methods and scales (Wimley-White for hydrophobicity, monoisotopic masses, Henderson-Hasselbalch for pH effects). The values are suitable for research and publication use.
The first value assumes all cysteines form disulfide bonds (cystines), which contribute 125 Mβ»ΒΉcmβ»ΒΉ per pair. The second value assumes all cysteines remain reduced (no disulfides). This gives you both oxidized and reduced scenarios.
Free PNG or JPG images are raster graphics that are generated at medium resolution (typically 150 DPI equivalent) and are larger than they appear on screen. Pro subscribers will have access to higher resolution (up to 600 dpi equivalent) PNG and JPG, as well as SVG, a vector-based format that can be scaled to any size without quality loss.
Sequence library features are in development! For now, you can bookmark or copy sequences. Future versions will include user accounts and saved sequence libraries.
Yes! PepDraw's core features are free for academic, educational, and research use. We're developing premium features for advanced users that will be part of a Pro tier.
Complete rebuild with real-time rendering engine, perfect ring geometry for aromatic residues, and enhanced pH-dependent visualization. Built with Python and modern web technologies.