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  • 1
    ISSN: 1520-510X
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 116 (1994), S. 5909-5915 
    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
    Springer
    Journal of molecular modeling 6 (2000), S. 539-549 
    ISSN: 0948-5023
    Keywords: Protein similarity ; Protein structure comparison ; Protein structure superposition ; Consensus alignment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The use of a Gaussian-based representation of protein structures for evaluating protein-structure similarities and deriving three-dimensional superpositions is presented. The approach, as implemented in the program GAPS, is applied to three pairs of proteins with different topological characteristics (rich α-helix, mixed α-helix/β-strand, and rich β-strand), low sequence identities (10–30%), and recognized difficulties to define a unique optimum alignment.Validation of the GAPS superpositions is done by comparison with superpositions obtained by the TOP, GA_FIT, and ALIGN programs and those directly extracted from the FSSP database. Results suggest that a Gaussian-based methodology offers an objective means to, depending on the Gaussian-based representation, derive a consensus three-dimensional superposition when alternative superposition solutions exist.
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 99 (1995), S. 10752-10758 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 104 (1996), S. 636-647 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A procedure based on quantum molecular similarity measures (QMSM) has been used to compare electron densities obtained from conventional ab initio and density functional methodologies at their respective optimized geometries. This method has been applied to a series of small molecules which have experimentally known properties and molecular bonds of diverse degrees of ionicity and covalency. Results show that in most cases the electron densities obtained from density functional methodologies are of a similar quality than post-Hartree–Fock generalized densities. For molecules where Hartree–Fock methodology yields erroneous results, the density functional methodology is shown to yield usually more accurate densities than those provided by the second order Møller–Plesset perturbation theory. © 1996 American Institute of Physics.
    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 107 (1997), S. 3576-3583 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A topological analysis of intracule and extracule densities and their Laplacians computed within the Hartree–Fock approximation is presented. The analysis of the density distributions reveals that among all possible electron–electron interactions in atoms and between atoms in molecules only very few are located rigorously as local maxima. In contrast, they are clearly identified as local minima in the topology of Laplacian maps. The conceptually different interpretation of intracule and extracule maps is also discussed in detail. An application example to the C2H2, C2H4, and C2H6 series of molecules is presented. © 1997 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of chemical information and modeling 34 (1994), S. 1047-1053 
    ISSN: 1520-5142
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Perspectives in drug discovery and design 20 (2000), S. 191-207 
    ISSN: 1573-9023
    Keywords: flexible ligand docking ; flexible ligand superposition ; molecular similarity ; thrombin ; virtual screening
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The development of similarity methods for fast flexible ligand superposition has recently received considerable attention. These efforts have brought similarity methods to a level of performance comparable to the well established protein-ligand docking methods for binding mode assessment and molecular database screening. However, the strengths and intrinsic limitations of both methodologies have been also stressed out extensively. As the number of resolved ligand-bound protein structures increases, combining ligand-based and receptor-based approaches emerges as a consensus strategy to maximally exploit the structural information available and improve the results obtained with either of the methods alone.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical chemistry accounts 99 (1998), S. 44-52 
    ISSN: 1432-2234
    Keywords: Key words: Quantum similarity ; Similarity measures and indices ; One-electron density ; Intracule and extracule densities ; Molecular alignment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. The calculation of quantum similarity measures from second-order density functions contracted to intracule and extracule densities obtained at the Hartree-Fock level is presented and applied to a series of atoms, (He, Li, Be, and Ne), isoelectronic molecules (C2H2, HCN, CNH, CO, and N2), and model hydrogen-transfer processes (H2/H+, H2/Hot, H2/H−). Second-order quantum similarity measures and indices are found to be suitable measures for quantitatively analyzing electron-pair density reorganizations in atoms, molecules, and chemical processes. For the molecular series, a comparative analysis between the topology of pairwise similarity functions as computed from one-electron, intracule, and extracule densities is carried out and the assignment of each particular local similarity maximum to a molecular alignment discussed. In the comparative study of the three hydrogen-transfer reactions considered, second-order quantum similarity indices are found to be more sensitive than first-order indices for analyzing the electron-density reorganization between the reactant complex and the transition state, thus providing additional insights for a better understanding of the mechanistic aspects of each process.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Journal of computer aided molecular design 13 (1999), S. 79-93 
    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
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