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Updated: Apr 24, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
De novo design of stable α-helices
Alexander Yakimov1, Georgy Rychkov, Michael Petukhov
1Department of Molecular and Radiation Biophysics, Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, 188300, Russia.
Abstract:
Recent studies have elucidated key principles governing folding and stability of α-helices in short peptides and globular proteins. In this chapter we review briefly those principles and describe a protocol for the de novo design of highly stable α-helixes using the SEQOPT algorithm. This algorithm is based on AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides, and the tunneling algorithm for global sequence optimization.
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