Interactions between CG beads in this method, adopting the similarįorms in the CHARMM atomistic force field, are described by bond,Īngle, 6–12 Leonnard-Jones and Coulomb potentials. Is efficiently reproduced with as small number of CG beads as possible. 12 In this CG model, a neural network like algorithm 13 is employed to determine the CG mapping of anĪtomistic protein structure. On the protein shapes while the later one is associated with specificĪmino acid residues of the proteins. In the case of proteins, the former approach is dependent Schemes of reducing an atomistic structure into a simplified representationįall into two major categories: shape-based (SB) and residue-based The levels of granularity and specific applications. The way of coarse-graining a protein is not unique, depending Of many mesoscopic scale phenomena that are inaccessible by atomistic The same time allow larger integration time steps for MD simulationsīecause of the elimination of fast motions, enabling the exploration Into a simplified model would alleviate computational costs and at 3− 5 As such, the reduction of an atomistic structure Through reducing the total number of degrees of freedom of the system
Processes, a variety of coarse-graining approaches have been suggested Of a molecular mechanics (MM)-based MD simulation to probe more biological Scales that are usually beyond the capability of atomistic molecularĭynamics (MD) simulation. Suitable for simulating complex biomolecular systems. In brief, the GBEMP model given here is general and transferable, The model was reflected by the excellent correlation between GBEMPĪnd AMOEBA models in the calculations of the dipole moment of peptides. In addition, the encouraging performance of As a result, the coarse-grained protein model presented anĪccurate description of nonbonded interactions (particularly electrostaticĬomponent) between hetero/homodimers (such as peptide–peptide, More importantly, unlike other coarse-grainedĪpproaches, our framework is based on the fundamental intermolecularįorces with explicit treatment of electrostatic and repulsion-dispersionįorces. Library), as well as from atomistic force field simulations (usingĪMOEBA, AMBER, and CHARMM force fields), while saving the computationalĬost by a factor of about 10–200 depending on specific casesĪnd atomistic models. Key features observed from experimental protein structures (Dunbrack We demonstrate that the anisotropicĬoarse-grained model, namely GBEMP model, is able to reproduce many Presenting a coarse-grained model for twenty kinds of amino acidsĪnd proteins, based on the anisotropic Gay–Berne and pointĮlectric multipole (EMP) potentials. Anisotropic potential has been widely used toĮvaluate the nonbonded interactions between coarse-grained particlesīeing described as elliptical rigid bodies.