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  • 1
    Title: Monte Carlo methods in chemical physics; 105
    Contributer: Ferguson, David M. , Siepmann, J. Ilja , Truhlar, Donald G.
    Publisher: Chichester u.a. :Wiley,
    Year of publication: 1999
    Pages: 555 S.
    Series Statement: Advances in chemical physics 105
    Type of Medium: Book
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  • 2
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 111 (1989), S. 4371-4378 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 114 (1992), S. 6555-6556 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    ISSN: 0948-5023
    Keywords: Keywords: Helix-helix interaction ; proline-containing helices ; bacteriorhodopsin ; G protein-coupled receptor.
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract A sequence analysis and comparison of transmembrane helices in bacteriorhodopsin (BR) and G protein-coupled receptors (GPCRs) is presented to identify potential regions of homology across protein families. The results show a common pattern of residues is conserved within the interhelical contact regions of BR that fit a knob-into-hole structural motif previously postulated for globular proteins and photosynthetic reaction centers. Based on an alignment of conserved prolines in transmembrane helices, it is inferred that analogous helix packing arrangements are possible in the rhodopsin-like GPCRs. Molecular models of GPCR helices V and VI indicate these interactions occur between aromatic and hydrophobic residues flanking the highly conserved prolines in these sequences. A similar packing arrangement is shown to occur in the X-ray structure of the melittin which also displays a unique pairing of proline-linked helices. The contact pattern identified is further applied to predict the packing of pairs of proline-containing helices in the pheromone-like and cAMP GPCRs. A potential role in stabilizing structure formation is also suggested for the contacts. The results and conclusions are supported by recent biophysical studies of zinc binding to kappa-opioid receptor mutants.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 99 (1993), S. 10086-10087 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Molecular dynamics free energy simulations have been performed on three solvated systems to examine the potential benefits of Bennett's acceptance ratio (AR) method [Bennett, J. Comput. Phys. 22, 245 (1976)], as compared to standard statistical perturbation techniques (FEP). The AR sampling equation has been implemented along with double-ended FEP sampling to calculate the relative solvation free energy of neon/nothing, neon/TIP3P-water and phenol/benzene in periodic TIP3P water. A histogram method is also introduced to calculate the overlap in the double-ended samples 〈E1−E0〉0 and 〈E0−E1〉1 from the density functions, p0(ΔE) and p1(ΔE), allowing window increments (δλ) to be correlated with % overlap and accuracy in the calculations. This relatively new concept is based on the fact that accuracy in both AR and FEP methods can be shown to depend on the overlap. The results indicate that the AR methodology has some advantages for calculating free energies when sample sizes are limited and minimal overlap exists in the ensemble samples at each window, mainly in reductions to the statistical errors. However, as more extensive simulations revealed, if the overlap in the density functions is increased (through reductions in window sizes), the simple FEP averages and variances approach near parity with the AR "best estimate'' results, indicating that the methods are effectively the same; with the caveat of adequate sampling.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of medicinal chemistry 34 (1991), S. 2654-2659 
    ISSN: 1520-4804
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Journal of global optimization 4 (1994), S. 209-227 
    ISSN: 1573-2916
    Keywords: Protein conformation ; molecular mechanics ; conformational searching
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract The conformational space of two protein structures has been examined using a stochastic search method in an effort to locate the global minimum conformation. In order to reduce this optimization problem to a tractable level, we have implemented a simplified force field representation of the protein structure that drastically reduces the degrees of freedom. The model replaces each ammo acid (containing many atoms) with a single sphere centered on the Cα position. These spheres are connected by virtual bonds, producing a “string of beads” model of the peptide chain. This model has been coupled with our stochastic search method to globally optimize the conformation of two common structural motifs found in proteins, a 22-residue α-helical hairpin and a 46-residue β-barrel. The search method described further reduces the optimization problem by taking advantage of the rotational isomerisms associated with molecular conformations and stochastically explores the energy surface using internal, torsional degrees of freedom. The approach proved to be highly efficient for globally optimizing the conformation of the α-helical hairpin and β-barrel structure on a moderately powered workstation. The results were further verified by applying variations in the search strategy that probed the low energy regions of conformational space near the suspected global minimum. Since this method also provides information regarding the low energy conformers, we have presented an analysis of the structures populated, and brief comparisons with other work. Finally, we applied the method to globally optimize the conformation of a 9-residue peptide fragment using a popular all-atom representation and successfully located the global minimum consistent with results from previous work.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 12 (1991), S. 620-626 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A protocol to replace “10-12” hydrogen bonding function with the “6-12” form to reproduce hydrogen bond distances, energies, and geometries in molecular mechanics calculations is described. The 6-12 function was least-squares fit to the normally employed 10-12 form of the function for the hydrogen bond types of the Weiner et al. force field by iterating over the A and B coefficients. A weighting function was used to fit the curves in the most critical areas. The 6-12 hydrogen bond model was compared with the Weiner et al. force field, OPLS/AMBER fore field, and quantum mechanical calculations on two simple systems, the water dimer and the chloride-water interaction. The 6-12 model produced structures, energies, and geometries that were consistent with the other molecular mechanics calculations and showed reasonable agreement to the quantum mechanical results for the water dimer. The 6-12 model was also compared with normal calculations using a 10-12 model on several representative systems. The results indicate that the 6-12 function, when substituted by the procedure outlined in this work, yields structures and hydrogen bond properties that are similar to the normal 10-12 model.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 70-79 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The gas-phase interaction energies of methane and neopentane dimers are calculated at various intermolecular distances and geometries using several molecular mechanics and semiempirical parameter sets. For comparisons, a set of reference calculations are also performed using the 6-311G (2d, 2 p) basis set with the inclusion of second-order Möller-Plesset energies (MP2) and basis set superposition corrections. These calculations are further used to examine the mechanism by which the AM1 and PM3 methods account for dispersion interactions in molecular systems. While no specific parameter(s) are included in semiempirical energy functions to capture such effects, the results indicate that both methods produce favorable interaction energies at near contact distances for the dimer systems. AM1 energies, however, show much closer agreement with the reference calculations, indicating potential deficiencies in the PM3 parameter set. Although the source of the dispersion energy could be traced to the attractive Gaussians of the core repulsion function in the AM1 Hamiltonian, a similar link could not be established for PM3. In contrast, PM3 dispersion energies apparently stem from a collection of contributions implicitly included during parameter optimization, providing no clear mechanism for correction or adjustment. Based on the analysis presented, an approach is also suggested for improving the AM1 parameter set. © 1997 by John Wiley & Sons, Inc.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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