Build · module 12
Biomolecule
Build an all-atom peptide from its one-letter sequence — helix, strand, PPII or coil, with termini and protonation at a pH — or a DNA or RNA strand.
Open it Build›Biomolecule…
- You start with
- A one-letter sequence or a FASTA file.
- You get
- An all-atom peptide or strand, cleaned up with UFF.
Step by step
Choose the mode
Peptide (default) or Nucleic acid.
Enter the sequence
One-letter codes, or Import FASTA. For a strand: DNA or RNA, written 5′ → 3′.
Set the secondary structure
α-helix, β-strand, PPII or coil, or your own φ, ψ and ω.
Termini and state
N-terminus NH₃⁺, NH₂ or acetyl; C-terminus COO⁻, COOH or N-methyl amide; side chains at pH 7, 4 or 10, or neutral; UFF clean-up or the placed geometry.
Build
Build peptide or Build strand; it opens as a new structure.
The same without the Studio
Every Studio page calls the same core as the caps command and the caps Python package, so a step you clicked can be repeated in a script.
caps peptide AEAAAKEAAAKA -o peptide.pdb --helix --ph 7from caps import build
p = build.peptide("AEAAAKEAAAKA", structure="HHHHHHHHHHHH")
p.save("peptide.pdb")
