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Updated: Jun 23, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
A minima hopping study of all-atom protein folding and structure prediction
Shantanu Roy1, Stefan Goedecker, Martin J Field
1Departement Physik, Universität Basel, Klingelbergstr. 82, 4056 Basel, Switzerland.
Abstract:
The minima hopping algorithm (MHOP) to find global minima on potential energy surfaces is used for protein structure prediction. The energy surface of the protein is represented with an all-atom OPLS force field and an implicit free energy solvation term. The system we studied here is the small 10-residue beta-hairpin mini-protein, chignolin. Starting from a completely extended structure, we found minima with <0.5 A rms coordinate deviation from the geometry-optimized native experimental conformation. A few lowest-energy conformations were used for the calculation of NMR-restraint violations and chemical shifts, and the local minima found during each run leading to the global minimum were connected to trace out a search pathway of the folding process.
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