2007
DOI: 10.1021/jp0727190
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A Coarse-Grained Protein−Protein Potential Derived from an All-Atom Force Field

Abstract: In order to study protein-protein nonbonded interactions, we present the development of a new reduced protein model that represents each amino acid residue with one to three coarse grains, whose physical properties are derived in a consistent bottom-up procedure from the higher-resolution all-atom AMBER force field. The resulting potential energy function is pairwise additive and includes distinct van-der-Waals and Coulombic terms. The van-der-Waals effective interactions are deduced from preliminary molecular… Show more

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Cited by 96 publications
(133 citation statements)
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“…In the absence of such data, molecular systems can be explored using coarse-grained calculations (see Ref. 62), which have become increasingly popular (54,59). We have employed the rather simple force field with implicit solvent and Coloumb electrostatics.…”
Section: Potentiation Of the Btz Block By Ca 2ϩmentioning
confidence: 99%
“…In the absence of such data, molecular systems can be explored using coarse-grained calculations (see Ref. 62), which have become increasingly popular (54,59). We have employed the rather simple force field with implicit solvent and Coloumb electrostatics.…”
Section: Potentiation Of the Btz Block By Ca 2ϩmentioning
confidence: 99%
“…Specifically, H is a component of amino acids which make up the backbone and are attached to the backbone. To describe the dynamics of amino acids in the backbone, a simplified potential between amino acids is often introduced 28,29 . Each amino acid is approximated by a single (heavy) atom or pseudo-atom.…”
Section: B Potentials In Proteinsmentioning
confidence: 99%
“…al. 28 and Ha-Duong 30 represent the CG potential by a repulsive (1/r 6 ) term plus a Gaussian attractive term. If the amino acid is charged there is also an electrostatic term.…”
Section: B Potentials In Proteinsmentioning
confidence: 99%
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“…These sites can be located on atoms [21,22], on geometric centers or centers of mass (COM) of groups of atoms in an amino acid (AA) [23][24][25][26][27][28], or on a combination of both [29][30][31][32]. Zhang et al [33] also proposed a method to define CGs as COMs of groups of contiguous Ca atoms that move in a highly correlated fashion.…”
Section: Introductionmentioning
confidence: 99%