A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins.

A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins. Research Abstract Details 

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A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins. Abstract Text:

Koji Ogata,Kenji Soejima,Junichi Higo,

We have developed a computational method of protein design to detect amino acid sequences that are adaptable to given main-chain coordinates of a protein. In this method, the selection of amino acid types employs a Metropolis Monte Carlo method with a scoring function in conjunction with the approximation of free energies computed from 3D structures. To compute the scoring function, a side-chain prediction using another Metropolis Monte Carlo method was performed to select structurally suitable side-chain conformations from a side-chain library. In total, two layers of Monte Carlo procedures were performed, first to select amino acid types (1st layer Monte Carlo) and then to predict side-chain conformations (2nd layers Monte Carlo). We applied this method to sequence design for the entire sequence on the SH3 domain, Protein G, and BPTI. The predicted sequences were similar to those of the wild-type proteins. We compared the results of the predictions with and without the 2nd layer Monte Carlo method. The results revealed that the two-layer Monte Carlo method produced better sequence similarity to the wild-type proteins than the one-layer method. Finally, we applied this method to neuraminidase of influenza virus. The results were consistent with the sequences identified from the isolated viruses.

A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins. Publishing Authors By Initials

K Ogata,K Soejima,J Higo,

For similar biochemical phenomena, metabolism, and nutrition: biochemical phenomena: molecular structure: molecular conformation: protein conformation: protein structure, tertiary: protein interaction domains and motifs: src homology domains research abstracts see: biochemical phenomena, metabolism, and nutrition: biochemical phenomena: molecular structure: molecular conformation: protein conformation: protein structure, tertiary: protein interaction domains and motifs: src homology domains research

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A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins. Journal Published:

PUBLICATION TYPE: Journal Article

Journal: Journal of biochemistry

VOLUME: 140

Page Numbers: 543-52

Journal Abbreviation: J. Biochem.

ISSN: 0021-924X

DAY: 31

MONTH: 08

YEAR: 2006

A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins. Information

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LANGUAGE: eng

NlmUniqueID: 376600

A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins. Keywords Mesh Terms:

KEYWORDS: src Homology Domains

MESH TERMS: chemistry

Chemical & Substance for Abstract: A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins. Information

Substance Name: Neuraminidase

Registry Number: EC 3.2.1.18

Grant and Affiliation Information for A Monte Carlo sampling method of amino acid sequences adaptable to given main-chain atoms in the proteins.

AFFILIATION: Centre for Computational Biology, The Hospital for Sick Children, 555 University Avenue, Toronot, Ontario M5G 1X8, Canada.

Country: Japan

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MEDLINETA: J Biochem

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