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  • 1
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 74-86 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: A possible application of a novel double-iterated Kalman filter (DIKF) as an algorithm for molecular structure determination is investigated in this work. Unlike traditional optimization algorithms, the DIKF does not exploit experimental nuclear magnetic resonance (NMR) constraints in a penalty function to be minimized but used them to filter the atomic coordinates. Furthermore, it is a nonlinear Bayesian estimator able to handle the uncertainty in the experimental data and in the computed structures, represented as covariance matrices. The algorithm presented applies all constraints simultaneously, in contrast with DIKF algorithms for structure determination found in literature, which apply the constraints one at a time. The performances of both paradigms are tested and compared with those obtained by a commonly used optimization algorithm (based on the conjugate gradient method). Besides providing estimates of the conformational uncertainty directly in the final covariance matrix, DIKF algorithms appear to generate structures with a better stereochemistry and be able to work with realistically imprecise constraints, while time performances are strongly affected by the heavy matricial calculations they require. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 2 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 156-166 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The structural stabilities of endo and exo conformations of retronecine and heliotridine molecules were analyzed using different ab initio, semiempirical, and molecular mechanics methods. All electron and pseudopotential ab initio calculations at the Hartree-Fock level of theory with 6-31G* and CEP-31G* basis sets provided structures in excellent agreement with available experimental results obtained from X-ray crystal structure and 1H-NMR (nuclear magnetic resonance) studies in D2O solutions. The exo conformations showed a greater stability for both molecules. The most significant difference between the calculations was found in the ring planarity of heliotridine, whose distortion was associated with the interaction between the O(11)H group and the C(1)-C(2) double bond as well as with a hydrogen bond between O(11)H and N(4). The discrepancy between pseudopotential and all-electron optimized geometries was reduced after inclusion of the innermost electrons of C(1), C(2), and N(4) in the core potential calculation. The MNDO, AM1, and PM3 semiempirical results showed poor agreement with experimental data. The five-membered rings were observed to be planar for AM1 and MNDO calculations. The PM3 calculations for exo-retronecine showed a greater stability than the endo conformer, in agreement with ab initio results. A good agreement was observed between MM3 and ab initio geometries, with small differences probably due to hydrogen bonds. While exo-retronecine was calculated to be more stable than the endo conformer, the MM3 calculations suggested that endo-heliotridine was slightly more stable than the exo form. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 418-428 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: An extended dynamic programming algorithm is presented that is applicable to the fragment assembly phase of the site mapping fragment assembly approach to peptide docking. After constructing a free energy map of the receptor using each of the amino acids in the peptides to be docked, we apply the algorithm to two systems: HIV-1 protease complexed with a synthetic hexameric inhibitor, and MHC HLA-A2 complexed with a nonameric peptide. The all atom root mean square deviation between the predicted and crystal structures was 1.7 and 2.0 Å, respectively. While these results are reasonable considering the relatively coarse level of mapping, the more important result is that the structures are probably very close to the best obtainable by an exhaustive search through the entire data map, and yet are obtained with a reduction of 3-5 orders of magnitude in the number of computations. We also outline a prescription for an iterative procedure which finds the global minimum with increasing confidence. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 3 Ill.
    Materialart: Digitale Medien
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  • 4
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 469-475 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Parallel computing seems to be the solution for molecular dynamics of large atomic systems, such as proteins in water environments, but the simulation time critically depends on the processor allocation strategy. A study of the optimal processor allocation based on a space decomposition algorithm for single instruction multiple data flow mesh computers is presented. A particular effort has been made to identify the best criterion according to which the atoms can be allocated to the processors using a spatial decomposition approach. The computing time depends on the granularity of the space decomposition among processing elements and on the ratio between the computation power of processing elements and the communication speed of the interprocessor network. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 385-385 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 806-820 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The self-consistent reaction field (SCRF) method proposed by Miertus, Scrocco, and Tomasi (MST) was extended to solutions of neutral solutes in CCl4. A detailed parametrization of the solute/solvent interface and of the “hardness” atomic parameters determining the van der Waals interactions was performed from comparison with experimental data and Monte Carlo simulations. The parametrization was carried out at both ab initio (6-31G*) and semiempirical (MNDO, AM1, PM3) levels. The MST/SCRF optimized versions provide accurate estimates of the free energy of solvation in CCl4 for the series of molecules studied. Furthermore, a precise description of the solvent effect on different chemical processes in CCl4 solution supports the reliability of the parametrization. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 7 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 940-953 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The multiparameter multistep relaxation (MPMSR) method, a routine within a new suite of parameterization programs entitled parameter analysis and refinement toolkit system (PARTS), was developed to assist in the development of molecular mechanics (MM3 and MM2) force field parameters and represents an ongoing effort in our laboratories to generate more accurate force fields in shorter times. In contrast to other computerized parameterization approaches, this method simulates intuition guided trial-and-error and has been used successfully within our laboratories to develop MM2 and MM3 force fields. The primary aim of this approach is to minimize human inspection time and effort, with simultaneous improvement in the efficiency and accuracy of the parameterization process. In an effort to validate the generality of the MPMSR method, a well parameterized data set of phosphine derivatives was reexamined. With the identical set of training molecules used in the original MM3 phosphine parameterization and with minimal human intervention, MPMSR shortened the process from several months to approximately five days. Although the previous phosphine force field is well parameterized, the newly generated MPMSR set of parameters has achieved an overall better fit to the experimentally observed data and ab initio calculations. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 15 Tab.
    Materialart: Digitale Medien
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  • 8
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 992-1001 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: The four-index transformation has a high ratio of data transfer to computation making it a potential “bottleneck” for parallel correlation energy determination. We present formulas for the communication times on different parallel architectures for an algorithm that is primarily designed for distributed-memory machines. We also implemented the algorithm on two shared-memory parallel computers, the Encore Multimax and the Alliant FX-8, and measured wall clock times for several problem sizes and processor configurations. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 5 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996), S. 1013-1024 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: Although no crystal structures of mixed-chain phosphatidylcholines with unsaturated sn-2 acyl chains exist, the force field method in conjunction with the experimentally determined structure of saturated identical-chain phosphatidylcholine can be applied to simulate molecular structure for mixed-chain phosphatidylcholines. In this study, the packing models of mixed-chain 1-palmitoyl-2-linoleoyl-phosphatidylcholines in bilayers at temperatures below the gel-liquid crystalline phase transition temperature or T 〈 Tm are simulated by using Allinger's MM3(92) force field. Our results indicate that the unsaturated sn-2 acyl chains of the mixed-chain lipid can fold into two energy-minimized topologies: the crankshaftlike and the U-shaped motifs. The folded region in the crankshiftlike sn-2 acyl chain is characterized by a sequence s- Δs+s+Δs-, and the U-shaped chain arises from the characteristic sequence s-Δs+s-Δs+, where s± denotes the ± skew conformation and Δ the cis carbon-carbon double bond. These modeled structures of 1-palmitoyl-2-linoleoyl-phosphatidylcholines in the bilayer at T 〈 Tm should not be regarded as highly rigid structures, since torsion angles of carbon-carbon bonds associated with sequences s Δs+s+Δs and s Δs+s-Δ s+ can fluctuate somewhat without appreciably affecting the steric energy of the corresponding lipid bilayer. © 1996 by John Wiley & Sons, Inc.
    Zusätzliches Material: 8 Ill.
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 17 (1996) 
    ISSN: 0192-8651
    Schlagwort(e): Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Materialart: Digitale Medien
    Standort Signatur Erwartet Verfügbarkeit
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