MolDraw › Chemistry tools › Peptide and DNA Sequence to Structure
Peptide and DNA Sequence to Structure
In short: Type a peptide sequence (one- or three-letter code) or a DNA or RNA sequence. You get the full structure as isomeric SMILES and a drawing, the molecular formula, monoisotopic and average mass, and for peptides the pI, charge and ε280; for DNA and RNA the GC content, complement and Tm.
Peptides are built from the 20 standard L-amino acids, N-terminus to C-terminus, with optional N-acetyl, C-amide, head-to-tail cyclisation and disulfide bonds. Oligonucleotides are built 5′ to 3′ on a 2-deoxyribose (DNA) or ribose (RNA) phosphodiester backbone with natural stereochemistry. Copy the SMILES, download a MOL or SDF file, or open the structure in the MolDraw editor.
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How to use the sequence to structure tool
- Choose Peptide or DNA or RNA.
- Type or paste the sequence. FASTA header lines, spaces, numbers and dashes are ignored. Peptides are read N- to C-terminus; DNA and RNA are read 5′ to 3′.
- Tick the options you need: N-terminal acetyl, C-terminal amide, Head-to-tail cyclic or Disulfide bonds for peptides, 5′-phosphate for oligonucleotides.
- Read the formula and masses. Use Copy SMILES, Download MOL, Download SDF or Open in MolDraw editor to take the structure further.
How a peptide structure is built
A peptide bond joins the carboxyl carbon of one amino acid to the amino nitrogen of the next, and one water is lost for each bond. A sequence is always written from the free amino end (the N-terminus) to the free carboxyl end (the C-terminus), so DF (Asp-Phe) and FD (Phe-Asp) are different molecules.
Formula = Σ residue formulas + H₂O residue = amino acid − H₂O
All alpha carbons are L, which is S by the CIP rules for every standard amino acid except cysteine (L-Cys is R because sulfur outranks the carboxyl). Glycine has no stereocentre. Isoleucine (2S,3S) and threonine (2S,3R) also get their side-chain stereocentre right.
| Option | Change to the structure | Change to the formula |
|---|---|---|
| N-terminal acetyl | CH₃C(=O)– on the first nitrogen | + C₂H₂O (+42.0106 Da) |
| C-terminal amide | –C(=O)NH₂ instead of –COOH | − O + NH (−0.9840 Da) |
| Head-to-tail cyclic | Extra peptide bond from the last C=O to the first N | − H₂O (−18.0106 Da) |
| Disulfide bond | S–S between two cysteines (paired in order) | − 2 H per bond (−2.0157 Da) |
pI, charge and extinction coefficient
The net charge is the sum over all ionisable groups. Each basic group contributes +1 / (1 + 10pH − pKa) and each acidic group −1 / (1 + 10pKa − pH). The EMBOSS pKa set is used: N-terminus 8.6, C-terminus 3.6, Asp 3.9, Glu 4.1, His 6.5, Cys 8.5, Tyr 10.1, Lys 10.8, Arg 12.5. The pI is the pH where the net charge is zero. Acetylated N-termini, amidated C-termini and cysteines in disulfides are not counted.
ε₂₈₀ = 5500 × n(Trp) + 1490 × n(Tyr) + 125 × n(cystine) M⁻¹ cm⁻¹
How a DNA or RNA structure is built
Each nucleotide is a base on carbon 1′ of a sugar: 2-deoxyribose in DNA, ribose (with a 2′-OH) in RNA. A phosphodiester bond links the 3′-oxygen of one sugar to the 5′-oxygen of the next through a phosphate, so a strand has a 5′ end and a 3′ end and is written 5′ to 3′. Bases are attached through N9 (A, G) or N1 (C, T, U) with the natural β-D configuration.
Formula = Σ nucleoside formulas + (N − 1) × (PO₂ − H) 5′-phosphate: + HPO₃
| Quantity | Formula used | When |
|---|---|---|
| GC content | (G + C) / N × 100 % | always |
| Tm, Wallace rule | 2 × (A + T) + 4 × (G + C) °C | fewer than 14 nt |
| Tm, basic GC formula | 64.9 + 41 × (G + C − 16.4) / N °C | 14 nt or more |
| Complement | A↔T (A↔U in RNA), G↔C, read 3′ to 5′ | always |
| Reverse complement | complement written 5′ to 3′ | always |
Structures are drawn for up to 30 residues or nucleotides. Longer sequences (up to 2000) still give the formula, masses and SMILES. Masses are for the neutral free acid; salts and modifications are not included.
Worked examples
Triglycine, GGG
3 × C₂H₅NO₂ − 2 H₂O.
C₆H₁₁N₃O₄, 189.0750 Da (mono), 189.17 g/mol
Asp-Phe (aspartame without its methyl ester)
C₄H₇NO₄ + C₉H₁₁NO₂ − H₂O. Aspartame itself is the methyl ester, C₁₄H₁₈N₂O₅.
C₁₃H₁₆N₂O₅, 280.1059 Da, pI 3.75
Angiotensin II, DRVYIHPF
Eight residues, one Tyr, so ε₂₈₀ = 1490 M⁻¹ cm⁻¹.
C₅₀H₇₁N₁₃O₁₂, 1045.5345 Da, [M+H]⁺ 1046.5418
Oxytocin, CYIQNPCLG-NH₂
Tick C-terminal amide and Disulfide bonds: Cys1–Cys6 ring.
C₄₃H₆₆N₁₂O₁₂S₂, 1007.19 g/mol
DNA 5′-ATGC-3′
4 deoxynucleosides + 3 phosphodiester links.
C₃₉H₅₀N₁₅O₂₂P₃, 1173.82 g/mol, GC 50 %, Tm 12 °C (Wallace)
M13 forward primer (17 nt)
5′-GTAAAACGACGGCCAGT-3′: 9 of 17 bases are G or C.
GC 52.9 %, Tm 47.1 °C (basic GC formula)
Common mistakes
- Writing a peptide C to N. Sequences always run from the N-terminus. YGGFL is Leu-enkephalin; LFGGY is a different peptide.
- Forgetting the water. A linear peptide is the sum of residue masses plus one H₂O (18.0106 Da mono). A cyclic peptide has no extra water.
- Mixing up mass types. Use monoisotopic mass for high-resolution MS peaks and average mass for weighing and molarity.
- Ignoring disulfides. Each S–S bond removes two hydrogens (−2.016 Da), which matters in MS.
- Using T in RNA or U in DNA. The tool flags the mismatch. Choose the right type first.
- Reading the complement 5′ to 3′. The plain complement runs 3′ to 5′. For a primer or probe you usually want the reverse complement.
- Using the Wallace rule for long primers. It overestimates Tm above about 14 nt. The tool switches to the GC formula there.
Want to label residues or draw a mechanism? Open the structure in MolDraw, the free online chemical structure editor, to add labels, arrows and colours, then export PNG or SVG.
Open MolDraw editorFrequently asked questions
How do I convert a peptide sequence to SMILES?
Type the sequence in one-letter (DRVYIHPF) or three-letter code (Asp-Arg-Val-Tyr-Ile-His-Pro-Phe). The tool joins the residues with peptide bonds from the N-terminus to the C-terminus and writes an isomeric SMILES with L stereochemistry at every alpha carbon except glycine.
What is the molecular formula of triglycine (GGG)?
Triglycine is C6H11N3O4. Three glycines (C2H5NO2 each) lose two waters when the two peptide bonds form. The monoisotopic mass is 189.0750 Da and the average mass is 189.17 g/mol.
What is the monoisotopic mass of angiotensin II?
Angiotensin II (DRVYIHPF) is C50H71N13O12 with a monoisotopic mass of 1045.5345 Da and an average mass of 1046.18 g/mol. Its [M+H]+ ion appears at m/z 1046.54.
How is the isoelectric point of a peptide estimated?
The tool adds the charges of the N-terminus, the C-terminus and the side chains of Asp, Glu, His, Cys, Tyr, Lys and Arg at each pH, using the EMBOSS pKa set. The pI is the pH where the net charge is zero. Real values can differ by 0.5 units or more.
How is the formula of a DNA oligonucleotide calculated?
Each nucleotide is a 2-deoxyribose with its base, and neighbours are joined by 3'-5' phosphodiester bonds. Adding the nucleosides and one HPO2 unit per link, minus one H, gives the formula. 5'-ATGC-3' with free 5' and 3' OH ends is C39H50N15O22P3, 1173.82 g/mol.
Which melting temperature formula does the tool use?
For fewer than 14 nucleotides it uses the Wallace rule, Tm = 2(A+T) + 4(G+C). For 14 or more it uses the basic GC formula, Tm = 64.9 + 41(G+C − 16.4)/N. Both are quick estimates for primers in typical PCR buffers.
What is the difference between the complement and the reverse complement?
The complement pairs each base (A with T or U, G with C) and is read 3' to 5'. The reverse complement is the same strand written 5' to 3'. For 5'-ATGC-3' the complement is 3'-TACG-5' and the reverse complement is 5'-GCAT-3'.
Why is my long sequence not drawn?
Structures are drawn for up to 30 residues or nucleotides, because larger drawings become unreadable. Longer sequences still give the full formula, masses and SMILES, up to 2000 residues.
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