Electron density fitting

BL Sibanda, TL Blundell, JM Thornton. Conformation of (I-hairpms m protein stractures A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 206 759-777, 1989. 

Nissink, J.W.M., Verdonk, M.L., Kroon, J., Mietzner, T., and Klebe, G. Superposition of molecules electron density fitting using fourier transforms. /. Comb. Chem. 1997, 38, 638-645. 

Accessing software for electron density fitting and structure validation... 

Thus, if it is assumed that the local virial theorem is valid for the model electron densities fitted to the experimental structure factors, the kinetic, g(r), and potential, v(r), energy densities may be mapped, as well as the energy characteristics of the (3,-1) bond critical points evaluated [38]. 

Except for occasional discussions of the basis set dependence of the results, the numerical implementation issues such as grid integration techniques, electron-density fitting, frozen-cores, pseudopotentials, and linear-scaling techniques, are omitted. 

Tel. 713-798-6565, fax 713-797-6718, e-mail faq dino.qci.bioch.bcm.tmc.edu Molecular graphics and crystallographic applications. Evans Sutherland. CHAIN is a newer, supported program for electron density fitting and molecular graphics that runs on Evans Sutherland (PS300s and ESVs) and Silicon Graphics. 

Constans, P. and Carbo, R. (1995). Atomic Shell Approximation Electron Density Fitting Algorithm Restricting Coefficients to Positive Values. JChem.Inf.Comput.Sci., 35,1046-1053. 

Fig. 10. (a) Frequency of helical backbone torsional angles in PDB structure with resolutions between 1 and 1.49 A resolution, (b) Difference plot between frequencies of helical backbone torsional angles in PDB structures with resolution between 1 and 1.49 A resolutions and those with resolutions between 2 and 2.49 A. Note loss of observations at O, = -61, -40 seen in high-resolution data and enhanced observations at classical (Pauling) ex-helical torsion angles (0, P = -57, -47) with lower-resolution data. The implication of this plot is that data from lower-resolution (>2 A) crystal structures of proteins is biased toward the classical alpha-helix because the electron density of the protein backbone is not adequately resolved by density data. In such cases, electron density fitting is usually supplemented by force field calculations that utilize monopole electrostatics. 

Constans P, Carbo R. Atomic shell approximation electron density fitting algorithm restricting coefficients to positive values. J Chem Inf Comput Sci 1995 35 1046-1053. 

Amat L, Carbo-Dorca RJ (2000) Molecular electronic density fitting using elementary Jacobi rotations under atomic shell approximation. Chem Inf Comput Sci 40 1188-1198... 

Approximation Electron Density Fitting Algorithm Restricting Coefficients to Positive Values. 

Electron Density Fitting Using Elementary Jacobi Rotations under Atomic Shell Approximation. 

H. M. Quiney. Electron density fitting for the Cotrlomb problem in relativistic density-functional theory. /. Chem. Phys., 124 (2006) 124104. 

If the studied crystals were perfectly ordered, then all the atoms would scatter in phase and the electron density map would have peaks at each of the atomic positions. However, in electron density maps of most protein atoms are not resolved from each another we need a model to be fitted to the electron density. Fitting models to density requires the use of computer graphics programs such as COOT (Emsley and Cowtan 2004) and as a result the electron density map is interpreted in terms of a set of atoms. In most cases the protein backbone is fitted first then, if the resolution permits, the side-chain atoms are positioned. The result is dependent on the resolution and the quality of the phases (O Fig. 30-1). Often regions of high flexibility (e.g., surface lysine side chains) are not visible since the corresponding electron density is smeared. 

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