Protein modelling and structure prediction with a reduced representation

• Autorzy: Kolinski A.
• Języki publikacji: EN

Abstrakty

EN

Protein modeling could be done on various levels of structural details, from simpli­fied lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular me­chanics. Here I describe a new high resolution reduced model, its force field and ap­plications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sam­pling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic pro­tein-like conformational biases, statistical potentials for the short-range confor- mational propensities, a model of the main chain hydrogen bonds and context-de­pendent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.

Słowa kluczowe

EN

protein modelling; protein folding; structure prediction; comparative modelling; lattice protein; Monte Carlo simulation

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2004
• Tom: 51
• Numer: 2
• Opis fizyczny: p.349-371,fig.,ref.

Twórcy

autor

Kolinski A.

• Warsaw University, L.Pasteura 1, 02-093 Warsaw, Poland

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