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Issue 38, 2011
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Coarse-grained force field: general folding theory

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Abstract

We review the coarse-grained UNited RESidue (UNRES) force field for the simulations of protein structure and dynamics, which is being developed in our laboratory over the last several years. UNRES is a physics-based force field, the prototype of which is defined as a potential of mean force of polypeptide chains in water, where all the degrees of freedom except the coordinates of α-carbon atoms and side-chain centers have been integrated out. We describe the initial implementation of UNRES to protein-structure prediction formulated as a search for the global minimum of the potential-energy function and its subsequent molecular dynamics and extensions of molecular-dynamics implementation, which enabled us to study protein-folding pathways and thermodynamics, as well as to reformulate the protein-structure prediction problem as a search for the conformational ensemble with the lowest free energy at temperatures below the folding-transition temperature. Applications of UNRES to study biological problems are also described.

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Publication details

The article was received on 14 Mar 2011, accepted on 06 May 2011 and first published on 03 Jun 2011


Article type: Perspective
DOI: 10.1039/C1CP20752K
Citation: Phys. Chem. Chem. Phys., 2011,13, 16890-16901
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    Coarse-grained force field: general folding theory

    A. Liwo, Y. He and H. A. Scheraga, Phys. Chem. Chem. Phys., 2011, 13, 16890
    DOI: 10.1039/C1CP20752K

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