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  • Molecular electrostatic potential  (8)
  • Springer  (8)
  • 1
    Electronic Resource
    Electronic Resource
    The atom assignment problem in automated de novo drug design. 2. A method for molecular graph and fragment perception (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 351-358 
    Details
    ISSN: 1573-4951
    Keywords: De novo drug design ; Molecular electrostatic potential ; Molecular graphs ; Molecular similarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary If atom assignment onto 3D molecular graphs is to be optimized, an efficient scheme for placement must be developed. The strategy adopted in this paper is to analyze the molecular graphs in terms of cyclical and non-cyclical nodes; the latter are further divided into terminal and non-terminal nodes. Molecular fragments, from a fragments database, are described in a similar way. A canonical numbering scheme for the fragments and the local subgraph of the molecular graph enables fragments to be placed efficiently onto the molecular graph. Further optimization is achieved by placing similar fragments into bins using a hashing scheme based on the canonical numbering. The graph perception algorithm is illustrated in detail.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00125176
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  • 2
    Electronic Resource
    Electronic Resource
    The atom assignment problem in automated de novo drug design. 5. Tests for envelope-directed fragment placement based on molecular similarity (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 457-462 
    Details
    ISSN: 1573-4951
    Keywords: De novo drug design ; Molecular electrostatic potential ; Molecular complementarity ; Molecular similarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The fragment placement method has been successfully extended to the problem of envelope-directed design. The atom assignment paradigm was based on molecular similarity between two molecular structures. A composite supersurface is defined to form the surface onto which the molecular fields are projected. The assignment process is then determined by using molecular similarity in the objective function to be optimized. In principle, this procedure is closely similar to that outlined in the previous paper for site-directed design. The rationale has been extensively tested on two benzodiazepine antagonists believed to bind to the same site.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00124003
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  • 3
    Electronic Resource
    Electronic Resource
    Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects (1994)
    Springer
    Journal of computer aided molecular design 8 (1994), S. 513-525 
    Details
    ISSN: 1573-4951
    Keywords: Drug design ; Molecular electrostatic potential ; MEP ; Dielectric
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Electrostatic interactions have always been considered an important factor governing ligand-receptor interactions. Previous work in this field has established the existence of electrostatic complementarity between the ligand and its receptor site. However, this property has not been treated rigorously, and the description remains largely qualitative. In this work, 34 data sets of high quality were chosen from the Brookhaven Protein Databank. The electrostatic complementarity has been calculated between the surface potentials; complementarity is absent between adjacent or neighbouring atoms of the ligand and the receptor. There is little difference between complementarities on the total ligand surface and the interfacial region. Altering the homogeneous dielectric to distance-dependent dielectrics reduces the complementarity slightly, but does not affect the pattern of complementarity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00123663
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  • 4
    Electronic Resource
    Electronic Resource
    The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 341-350 
    Details
    ISSN: 1573-4951
    Keywords: De novo drug design ; Molecular electrostatic potential ; Molecular complementarity ; Molecular similarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary This paper is the first of a series which examines the problems of atom assignment in automated de novo drug design. In subsequent papers, a combinatoric optimization method for fragment placement onto 3D molecular graphs is provided. Molecules are built from molecular graphs by placing fragments onto the graph. Here we examine the transferability of atomic residual charge, by fragment placement, with respect to the electrostatic potential. This transferability has been tested on 478 molecular structures extracted from the Cambridge Structural Database. The correlation found between the electrostatic potential computed from composite fragments and that computed for the whole molecule was encouraging, except for extended conjugated systems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00125175
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  • 5
    Electronic Resource
    Electronic Resource
    The atom assignment problem in automated de novo drug design. 4. Tests for site-directed fragment placement based on molecular complementarity (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 448-456 
    Details
    ISSN: 1573-4951
    Keywords: De novo drug design ; Molecular electrostatic potential ; Molecular complementarity ; Molecular similarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Three previous papers in this series have outlined an optimization method for atom assignment in drug design using fragment placement. In this paper the procedure is rigorously tested on a selection of five ligand-protein co-crystals. The algorithm is presented with the molecular graph of the ligand, and the electrostatic/hydrophobic potential of the site, with the aim of creating a placement on the molecular graph which is as electrostatically complementary or hydrophobically similar to the site as possible. Various designer options were tested, including, where appropriate, hydrogen bonding and a restricted number of halogens. In most cases, the placement obtained was at least as good as the native ligand, if not significantly better.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00124002
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  • 6
    Electronic Resource
    Electronic Resource
    Electrostatic complementarity between proteins and ligands. 2. Ligand moieties (1994)
    Springer
    Journal of computer aided molecular design 8 (1994), S. 527-544 
    Details
    ISSN: 1573-4951
    Keywords: Drug design ; Molecular electrostatic potential ; MEP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Drug design strategies consider factors governing intermolecular interactions to build up putative ligands. In many strategies, the ligand is constructed using fragments which are placed in the site sequentially. The optimization is then performed with each fragment. We would like to examine if this optimization strategy could generate ligands with optimal electrostatic interactions. The electrostatic complementarities between constituent moieties and the receptor site have been calculated. The whole-ligand complementarity does not appear to be the mathematical mean of the individual complementarities, nor have we found a simple relationship between the moiety and whole-ligand complementarities. The results demonstrate clearly that, using a simple model, it is very difficult to predict the electrostatic potential complementarity of the whole ligand from the complementarities of its constituent chemical moieties. This means that ligand design strategies must optimize the electrostatic complementarity globally, and not moiety by moiety.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00123664
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  • 7
    Electronic Resource
    Electronic Resource
    Electrostatic complementarity between proteins and ligands. 3. Structural basis (1994)
    Springer
    Journal of computer aided molecular design 8 (1994), S. 545-564 
    Details
    ISSN: 1573-4951
    Keywords: Drug design ; Molecular electrostatic potential ; MEP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Electrostatic potential complementarity between ligands and their receptor sites is evaluated by the superposition of the electrostatic potential, generated by the receptor, onto the ligand potential over the ligand van der Waals surface. We would like to examine which structural factors generate this pattern of superposition. Example studies suggest that in many ligand-protein pairs, there exist principal formal charges on each molecule, largely responsible for the electrostatic potential complementarity observed. Electrostatic potential complementarity depends on the relative disposition of these principal charges and the ligand van der Waals surface. Simple mathematical models were constructed to predict the complementarity solely from structural considerations. The essential conditions for electrostatic potential complementarity were elucidated. These can be used in ligand design strategies to obtain an electrostatically optimal ligand.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00123665
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  • 8
    Electronic Resource
    Electronic Resource
    The atom assignment problem in automated de novo drug design. 3. Algorithms for optimization of fragment placement onto 3D molecular graphs (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 359-372 
    Details
    ISSN: 1573-4951
    Keywords: De novo drug design ; Simulated annealing ; Molecular graphs ; Molecular electrostatic potential ; Molecular complementarity ; Molecular similarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Atom assignment onto 3D molecular graphs is a combinatoric problem in discrete space. If atoms are to be placed efficiently on molecular graphs produced in drug binding sites, the assignment must be optimized. An algorithm, based on simulated annealing, is presented for efficient optimization of fragment placement. Extensive tests of the method have been performed on five ligands taken from the Protein Data Bank. The algorithm is presented with the ligand graph and the electrostatic potential as input. Self placement of molecular fragments was monitored as an objective test. A hydrogen-bond option was also included, to enable the user to highlight specific needs. The algorithm performed well in the optimization, with successful replications. In some cases, a modification was necessary to reduce the tendency to give multiple halogenated structures. This optimization procedure should prove useful for automated de novo drug design.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00125177
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