High coordination lattice models of protein structure, dynamics and thermodynamics

Kolinski, A; Skolnick, J.

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Artykuł - szczegóły

Czasopismo

Acta Biochimica Polonica

1997 | 44 | 3 |

Tytuł artykułu

High coordination lattice models of protein structure, dynamics and thermodynamics

Autorzy

Kolinski A. , Skolnick J.

Warianty tytułu

Języki publikacji

Abstrakty

A high coordination lattice discretization of protein conformational space is described. The model allows discrete representation of polypeptide chains of globular proteins and small macromolecular assemblies with an accuracy comparable to the accuracy of crystallographic structures. Knowledge based force Held, that consists of sequence specific short range interactions, cooperative model of hydrogen bond network and tertiary one body, two body and multibody interactions, is outlined and discussed. A model of stochastic dynamics for these protein models is also described. The proposed method enables moderate resolution tertiary structure prediction of simple and small globular proteins. Its applicability in structure prediction increases significantly when evolutionary information is exploited or/and when sparse experimental data are available. The model responds correctly to sequence mutations and could be used at early stages of a computer aided protein design and protein redesign. Computational speed, associated with the discrete structure of the model, enables studies of the long time dynamics of polypeptides and proteins and quite detailed theoretical studies of thermodynamics of nontrivial protein models.

Słowa kluczowe

protein folding prediction protein thermodynamics protein structure lattice protein protein model Monte Carlo method protein dynamics

Wydawca

Czasopismo

Acta Biochimica Polonica

Rocznik

1997

Tom

Numer

Opis fizyczny

p.389-422,fig.

Twórcy

autor

Kolinski A.

University of Warsaw, L.Pasteura 1, 02-093 Warsaw, Poland; E-mail: Kolinski@chem.uw.edu.pl

autor

Skolnick J.

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