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M. Khalili, J.A. Saunders, A. Liwo, S. Oldziej, and H.A. Scheraga A united residue force-field for calcium-protein interactions Protein Sci 13 2004 2725 2735 The last of a series of papers describing the development and optimization of the UNRES (united-residue) model, which was derived by Scheraga and co-workers over the past few years. The beads are located on the Cα atom, on the centroid of the sidechain and on a 'peptide' (p) center located midway between two Cα atoms. However, Cα is only used to calculate the position of p; thus, the degrees of freedom correspond to a two-bead model. The parameterization is based on the statistical analysis of structures and on fitting the free energy functions obtained from full-atom simulations of oligopeptides. Additional terms account for correlation between the degrees of freedom. The model has been recently optimized to include ellipsoid sidechains and interaction parameters with calcium, and used in protein structure and interaction prediction.
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M. Zacharias Protein docking with a reduced protein model accounting for side-chain flexibility Protein Sci 12 2003 1271 1282 A model with one bead for the Cα atom and up to two beads for the sidechains was used in a protein-protein docking approach. Size and hydrophilic/hydrophobic interactions are accounted for by van der Waals like amino-acid-specific terms. Sidechain conformational changes are taken into account by introducing several different rotamers of the sidechain during docking. This procedure is shown to generate more accurate complex structures than rigid docking.
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α coarse graining J Mol Graph Model 22 2004 183 193 A new method for modeling a system as a set of rigid bodies connected by an elastic network is presented that reduces considerably the number of degrees of freedom with respect to conventional elastic network approaches. It is shown that the lowest modes of the system are reproduced with a good accuracy.
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