Orientation-dependent potential of mean force for protein folding
نویسندگان
چکیده
منابع مشابه
Orientation-dependent potential of mean force for protein folding.
We present a solvent-implicit minimalistic model potential among the amino acid residues of proteins, obtained by using the known native structures [deposited in the Protein Data Bank (PDB)]. In this model, the amino acid side chains are represented by a single ellipsoidal site, defined by the group of atoms about the center of mass of the side chain. These ellipsoidal sites interact with other...
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Extracting knowledge-based statistical potential from known structures of proteins is proved to be a simple, effective method to obtain an approximate free-energy function. However, the different compositions of amino acid residues at the core, the surface, and the binding interface of proteins prohibited the establishment of a unified statistical potential for folding and binding despite the f...
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There has been a great deal of activity recently on approaches to the calculation of protein folding using specially devised empirical potential functions. We have developed one such function that solves the protein structure recognition problem: given the sequence for a globular protein and a collection of plausible protein conformations, including the native conformation for that sequence, id...
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In a statistical approach to protein structure analysis, Miyazawa and Jernigan (MJ) derived a 20 × 20 matrix of inter-residue contact energies between different types of amino acids. Using the method of eigenvalue decomposition, we find that the MJ matrix can be accurately reconstructed from its first two principal component vectors as Mij = C0 + C1(qi + qj) + C2qiqj , with constant C’s, and 20...
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ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2005
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.1940058