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Updated: Jun 24, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
Determination of pair-wise inter-residue interaction forces from folding pathways and their implementation in
Sefer Baday1, Burak Erman, Yaman Arkun
1Department of Chemical and Biological Engineering, Koc University, Rumeli Feneri Yolu, 34450 Sariyer, Istanbul, Turkey.
Abstract:
Interaction forces among residue pairs are determined from optimum folding pathways along which a protein represented as a coarse-grained chain of alpha-carbons goes from different initial configurations to a known native state. A dynamic optimization approach is employed that uses the coarse-grained model to compute the optimal folding pathways. The pair-wise interaction forces obtained in this manner are incorporated into the coarse-grained model which is then simulated to fold the protein from a new set of initial configurations in a predictive way. We show that the folding pathways predicted in this manner are near-optimal. We applied the technique to the secondary structures: helix and beta-sheet.
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