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  • Title: Assembly of protein tertiary structures from secondary structures using optimized potentials.
    Author: Hoang TX, Seno F, Banavar JR, Cieplak M, Maritan A.
    Journal: Proteins; 2003 Aug 01; 52(2):155-65. PubMed ID: 12833540.
    Abstract:
    We present a simulated annealing-based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron-based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 A in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 A and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 A.
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