Determination of distributed polarizabilities to be used for peptide modeling

Voisin, Christophe; Cartier, Alain

doi:10.1016/0166-1280(93)87149-8

Cited by 28 publications

(22 citation statements)

References 24 publications

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“…Molecular geometries have been optimized with MMID2. The radius of SWNT model R increases with the number of rings around a section of SWNT, n. However, R is almost constant for SWNTs with different number of atoms in its length but with equal n. Contrary to the POLAR results, the PAPID [30] references increase monotonically with R. The values computed with POLAR for C 28 -C 48 , C 42 -C 72 and C 90 -C 120 models are greater than those obtained with PAPID reference by factors of 2, 3 and 5, respectively. In particular, for C 90 (9, 0) SWNT model, PAPID α = 1.130 Å 3 is in line with the reference (1.304 Å 3 ) by Jensen et al [10].…”

Section: Calculation Results and Discussioncontrasting

confidence: 76%

Effect of size and deformation on polarizabilities of carbon nanotubes from atomic increments

Torrens

2004

Future Generation Computer Systems

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Section: Calculation Results and Discussioncontrasting

confidence: 76%

Effect of size and deformation on polarizabilities of carbon nanotubes from atomic increments

Torrens

2004

Future Generation Computer Systems

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“…16,17 Past approaches to modeling MM polarization include those based around a fluctuating charge model, [18][19][20][21][22] those based on a Drude Oscillator model [23][24][25][26][27] and those based around induced dipoles. [28][29][30][31][32][33][34][35][36][37][38][39][40][41][42] The latter approach is the most widespread, and the SIBFA implementation 43 is one of a small number of programs with a long track record in terms of application to ligand-receptor interactions. Other recent specific approaches to polarization are reviewed elsewhere.…”

Section: Introductionmentioning

confidence: 99%

Assessing the Role of Polarization in Docking

et al. 2008

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We describe a strategy for including ligand and protein polarization in docking that is based on the conversion of induced dipoles to induced charges. Induced charges have a distinct advantage in that they are readily implemented into a number of different computer programs, including many docking programs and hybrid QM/MM programs; induced charges are also more readily interpreted. In this study, the ligand was treated quantum mechanically to avoid parametrization issues and was polarized by the target protein, which was treated as a set of point charges. The induced dipole at a given target atom, due to polarization by the ligand and neighboring residues, was reformulated as induced charges at the given atom and its bonded neighbors, and these were allowed to repolarize the ligand in an iterative manner. The final set of polarized charges was evaluated in docking using AutoDock 4.0 on 12 protein-ligand systems against the default empirical Gasteiger charges, and against nonpolarized and partially polarized potential-derived charges. One advantage of AutoDock is that the best rmsd structure can be identified not only from the lowest energy pose but also from the largest cluster of poses. Inclusion of polarization does not always lead to the lowest energy pose having a lower rmsd, because docking is designed by necessity to be rapid rather than accurate. However, whenever an improvement in methodology, corresponding to a more thorough treatment of polarization, resulted in an increased cluster size, then there was also a corresponding decrease in the rmsd. The options for implementing polarization within a purely classical docking framework are discussed.2008112

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“…The new values give polarizability tensors in good agreement with experiment, and the parameters ~ were found to be transferable to a range of molecules [25,26]. The resulting polarizability tensor and that obtained experimentally are given in table 1.…”

Section: Calculation O F Far-infrared Spectra From the Molecular Dynamentioning

confidence: 59%

“…In this way a unified charge model that reproduces both the dynamics and the farinfrared absorption might be obtained. Finally, we note that it has been shown that the atomic polarizabilities derived using the present method are transferable to a range of molecules [25,26]. This opens up the possibility of applying the method to many systems, including large, flexible macromolecules for which a molecular polarizability matrix method would not be useful.…”

Section: Resultsmentioning

confidence: 91%

Molecular dynamics analysis of charge fluctuations associated with far-infrared absorption in water

Souaille

Smith

1996

Molecular Physics

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Far-infrared absorption spectroscopy gives information on the charge fluctuations associated with hydrogen-bond dynamics in water. Here, we examine these fluctuations by calculating spectra from molecular dynamics simulations and comparing with experiment. Permanent and induced dipoles are included in the calculation of the system dipole moment. The induced dipoles are calculated on each atom using an iterative method that leads to self-consistency of the induced dipole contribution to the local field. The experimental far-infrared spectrum has two prominent bands, at ,,~ 600 cm -1 and ~ 200 cm -1, due to hydrogen-bond libration and stretching, respectively, The librational band is found to arise from fluctuations of the positions of the permanent charges in the simulation, whereas the stretching band originates from induced dipole fluctuations. The use of the self-consistent method enhances the intensity of the stretching peak relative to a non-iterative method, producing improved agreement with experiment. The frequency of the librational band is influenced significantly by long-range electrostatic interactions in the potential function. In contrast, the induced dipole fluctuations are relatively insensitive to the long-range effects; the effective isotropy of the molecular polarizability tensor is found to lead to a decoupling of the induced dipole fluctuations from the dynamical intermolecular orientational correlations of the permanent dipoles.

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Determination of distributed polarizabilities to be used for peptide modeling

Cited by 28 publications

References 24 publications

Effect of size and deformation on polarizabilities of carbon nanotubes from atomic increments

Effect of size and deformation on polarizabilities of carbon nanotubes from atomic increments

Assessing the Role of Polarization in Docking

Molecular dynamics analysis of charge fluctuations associated with far-infrared absorption in water

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