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  • 1
    Electronic Resource
    Electronic Resource
    A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors. 2. The relationship between alignment solutions obtained from conformationally rigid and flexible matching (2000)
    Springer
    Journal of computer aided molecular design 14 (2000), S. 39-51 
    Details
    ISSN: 1573-4951
    Keywords: flexible-conformations ; molecular alignments ; molecular-field similarity ; non-nucleoside HIV-1 reverse transcriptase inhibitors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract An analysis of the relationship among alignment solutions obtained from field-based matching of a representative set of rigid conformers of three non-nucleoside HIV-1 reverse transcriptase inhibitors and solutions obtained from flexible matching of the same conformers is presented. In some cases, different alignment solutions obtained from rigid matching converge to the same solution when conformational rigidity is relaxed, indicating that a reduced set of conformers per molecule may be sufficient in many field-based similarity studies. Furthermore, the results also indicate the importance of going beyond the pairwise similarity level to obtain consistent solutions in flexible-matching studies. In this respect, the best conformationally flexible multi-molecule alignment obtained is found to be in good agreement with the relative binding geometry and orientation found experimentally from protein-ligand crystal structures. The rms separation between corresponding atoms in computed and `experimental' sets of three inhibitor structures is 0.94 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008168228728
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  • 2
    Electronic Resource
    Electronic Resource
    A molecular-field-based similarity study of non-nucleoside HIV-1 reverse transcriptase inhibitors (1999)
    Springer
    Journal of computer aided molecular design 13 (1999), S. 79-93 
    Details
    ISSN: 1573-4951
    Keywords: molecular alignments ; molecular-field similarity ; non-nucleoside HIV-1 reverse transcriptase inhibitors ; pharmacophore patterns ; protein structure alignments
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract This article describes a molecular-field-based similarity method for aligning molecules by matching their steric and electrostatic fields and an application of the method to the alignment of three structurally diverse non-nucleoside HIV-1 reverse transcriptase inhibitors. A brief description of the method, as implemented in the program MIMIC, is presented, including a discussion of pairwise and multi-molecule similarity-based matching. The application provides an example that illustrates how relative binding orientations of molecules can be determined in the absence of detailed structural information on their target protein. In the particular system studied here, availability of the X-ray crystal structures of the respective ligand–protein complexes provides a means for constructing an 'experimental model' of the relative binding orientations of the three inhibitors. The experimental model is derived by using MIMIC to align the steric fields of the three protein P66 subunit main chains, producing an overlay with a 1.41 Å average rms distance between the corresponding Cα's in the three chains. The inter-chain residue similarities for the backbone structures show that the main-chain conformations are conserved in the region of the inhibitor-binding site, with the major deviations located primarily in the 'finger' and RNase H regions. The resulting inhibitor structure overlay provides an experimental-based model that can be used to evaluate the quality of the direct a priori inhibitor alignment obtained using MIMIC. It is found that the 'best' pairwise alignments do not always correspond to the experimental model alignments. Therefore, simply combining the best pairwise alignments will not necessarily produce the optimal multi-molecule alignment. However, the best simultaneous three-molecule alignment was found to reproduce the experimental inhibitor alignment model. A pairwise consistency index has been derived which gauges the quality of combining the pairwise alignments and aids in efficiently forming the optimal multi-molecule alignment analysis. Two post-alignment procedures are described that provide information on feature-based and field-based pharmacophoric patterns. The former corresponds to traditional pharmacophore models and is derived from the contribution of individual atoms to the total similarity. The latter is based on molecular regions rather than atoms and is constructed by computing the percent contribution to the similarity of individual points in a regular lattice surrounding the molecules, which when contoured and colored visually depict regions of highly conserved similarity. A discussion of how the information provided by each of the procedures is useful in drug design is also presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008098215954
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  • 3
    Electronic Resource
    Electronic Resource
    Intrinsic reaction coordinate of perturbed potential energy surfaces: Construction of perturbed energy profiles (1993)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 47 (1993), S. 307-317 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This contribution analyzes the changes in the intrinsic reaction coordinate (IRC) and in the potential energy profiles (PEP) caused by application of a uniform electric field evaluated using standard ab initio MO methods. Two typical organic processes have been studied, namely, the Friedel-Crafts and the Walden inversion reactions, which are modeled by suitable simple systems. The results for the Walden inversion reaction show that the IRC for the field-free and that for perturbed processes are almost coincident; in this case, using the field-free IRC to compute the perturbed energy profile is a very good approximation. On the contrary, for the Friedel-Crafts model reaction, the two IRCs differ slightly, so the energy profiles using the perturbed and the unperturbed IRCs are somewhat different. © 1993 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560470404
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  • 4
    Electronic Resource
    Electronic Resource
    The use of ab initio quantum molecular self-similarity measures to analyze electronic charge density distributions (1996)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 58 (1996), S. 361-372 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Exact quantum molecular overlaplike and Coulomb-like self-similarity measures are studied in a selected series of molecules with the same number of electrons. It is found that quantum molecular overlap self-similarity measures can be used to estimate the concentration of electronic charge in molecules. A good linear relationship between the overlap self-similarity measure and the volume is found for molecules with the same number of electrons when the atoms of the systems being compared belong to the same row of the periodic table. Finally, an upper bound for the quantum molecular overlap self-similarity measure of molecules with a number of electrons up to 54 is given from the atomic quantum self-similarity measures obtained using Slater-type functions. © 1996 John Wiley & Sons, Inc.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Genetic algorithms: A robust scheme for geometry optimizations and global minimum structure problems (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 16 (1995), S. 729-742 
    Details
    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 Genetic Algorithm for Geometry Optimizations (GALGO) program has been developed to study the efficiency of this method of finding global minimum structures. Using a semiempirical tight-binding potential, the behavior of different genetic algorithm (GA) operators has been tested for the linear chain isomer of a C8 cluster. An optimum set of parameters for the GA operators is proposed for this problem and afterward is used to obtain the global minimum structure of rare-gas atomic clusters of up to 13 atoms using the 12-6 Lennard-Jones interatomic pair potential. © 1995 by John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540160609
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  • 6
    Electronic Resource
    Electronic Resource
    On the calculation of ab initio quantum molecular similarities for large systems: Fitting the electron density (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 1113-1120 
    Details
    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 set of procedures for rapid calculation of quantum molecular similarities from ab initio wave functions is discussed. In all cases a density fitting is carried out to eliminate the need of calculating costly four-centered integrals. It is proved that this methodology can be applied to large systems to reproduce exact quantum molecular similarity measures at an extremely low computational cost. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540151007
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