Philipp E. Schilling

Ligation site finder

Paste a protein sequence to find chemoselective ligation sites for chemical protein synthesis — native chemical ligation (NCL), KAHA ligation, KAT ligation and serine/threonine ligation (STL) — plus common solid-phase peptide synthesis (SPPS) liabilities. Everything runs in your browser; nothing is uploaded.

Ligation sites

Native chemical ligation (NCL) [ref]
KAHA ligation [ref]
KAT ligation [ref]
Serine / threonine ligation (STL) [ref]

SPPS considerations

Pseudoprolines
Aspartimide-prone motifs

How it works

Each ligation chemistry joins two unprotected peptide segments at a junction defined by the N-terminal residue of the second segment: NCL at Xaa–Cys, NCL after desulfurization at Xaa–Ala, serine/threonine ligation at Xaa–Ser or Xaa–Thr, KAHA ligation at the residue installed by the hydroxylamine monomer, and KAT ligation at Leu–Gly or Phe–Gly. The tool scans every position — so consecutive and overlapping sites are all reported — and marks each junction with a bar (⎷) before the start of the second segment. SPPS motifs are highlighted without a junction marker.

How to cite

Schilling, P. E. Ligation site finder. https://schillingp.com/tools/ligation-site-finder/ (accessed [date]).

A citable version with a DOI is planned (Zenodo). The KAT ligation chemistry is described in Schilling, Steiner & Bode, Science 2026.