Figure 1 | Scientific Reports

Figure 1

From: Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein

Figure 1

A flowchart of Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to predict the structures of small peptides.

It shows the prediction process of small peptides structures in details. First, a full extended conformation of the peptide was built by Accelrys Discovery Studio2.5 from the primary sequence. Second, large scale structure sampling was performed through energy minimization, simulating annealing and refined MD simulation to produce a large number of structures. Third, the stereochemical qualities of those structures were evaluated and about 20% of the total is screened out. Fourth, the structures with better stereochemical qualities were screened by clustering.

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