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  • Drug design  (11)
  • Molecular electrostatic potential  (8)
  • Springer  (16)
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  • Springer  (16)
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  • 1
    Electronic Resource
    Electronic Resource
    Hydration in drug design. 2. Influence of local site surface shape on water binding (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 513-520 
    Details
    ISSN: 1573-4951
    Keywords: Drug design ; Hydration ; Protein-ligand complex ; Deep grooves ; Shallow grooves
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary If water molecules are strongly bound at a protein-ligand interface, they are unlikely to be displaced during ligand binding. Such water molecules can change the shape of the ligand binding site and thus affect strategies for drug design. To understand the nature of water binding, and factors influencing it, water molecules at the ligand binding sites of 26 high-resolution protein-ligand complexes have been examined here. Water molecules bound in deep grooves and cavities between the protein and the ligand are located in the indentations on the protein-site surface, but not in the indentations on the ligand surface. The majority of the water molecules bound in deep indentations on the protein-site surface make multiple polar contacts with the protein surface. This may indicate a strong binding of water molecules in deep indentations on protein-site surfaces. The local shape of the site surface may influence the binding of water molecules that mediate protein-ligand interactions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00124322
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  • 2
    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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  • 3
    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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  • 4
    Electronic Resource
    Electronic Resource
    Molecular surface-volume and property matching to superpose flexible dissimilar molecules (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 479-490 
    Details
    ISSN: 1573-4951
    Keywords: Molecular similarity ; Simulated annealing ; Hydrogen bonding ; Electrostatic potential ; Molecular skin ; Drug design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Steric complementarity is a prerequisite for ligand-receptor recognition; this implies that drugs with a common receptor binding site should possess sterically similar binding surfaces. This principle is used as the basis for an automatic and unbiased method that superposes molecules. One molecule is rotated and translated to maximize the overlap between the two molecular surface volumes. A fast grid-based method is used to determine the extent of this overlap, and this is optimized using simulated annealing. Matches with high steric similarity scores are then sorted on the basis of both hydrogen-bond and electrostatic similarity between the matched molecules. Flexible molecules are treated as a set of rigid representative conformers. The algorithm has correctly predicted superpositions between a number of pairs of molecules, according to crystallographic data from ligands that have been co-crystallized at common enzyme binding sites.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00124319
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  • 5
    Electronic Resource
    Electronic Resource
    Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions (1995)
    Springer
    Journal of computer aided molecular design 9 (1995), S. 500-512 
    Details
    ISSN: 1573-4951
    Keywords: Drug design ; Hydration ; Hydrogen bonds ; Protein-ligand complexes ; Water networks
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Water is known to play an important rôle in the recognition and stabilization of the interaction between a ligand and its site. This has important implications for drug design. Analyses of 19 high-resolution crystal structures of protein-ligand complexes reveal the multiple hydrogen-bonding feature of water molecules mediating protein-ligand interactions. Most of the water molecules (nearly 80%) involved in bridging the protein and the ligand can make three or more hydrogen bonds when distance and bond angles are used as criteria to define hydrogen-bonding interactions. Isotropic B-factors have been used to take into account the mobility of water molecules. The water molecules at binding sites bridge the protein and ligand, and interact with other water molecules to form a complex network of interconnecting hydrogen bonds. Some water molecules at the site do not directly bridge between the protein and the ligand, but may contribute indirectly to the stability of the complex by holding bridging water molecules in the right position through a network of hydrogen bonds. These water networks are probably crucial for the stability of the protein-ligand complex and are important for any site-directed drug design strategies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00124321
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  • 6
    Electronic Resource
    Electronic Resource
    Automated site-directed drug design: An assessment of the transferability of atomic residual charges (CNDO) for molecular fragments (1992)
    Springer
    Journal of computer aided molecular design 6 (1992), S. 407-426 
    Details
    ISSN: 1573-4951
    Keywords: Drug design ; Molecular fragments ; Atomic charges
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary In this paper a database of atomic residual charges has been constructed for all the molecular fragments defined previously in a combinatorial search of the Cambridge Structural Database. The charges generated for the atoms in each fragment are compared with charges calculated for whole molecules containing those fragments. The fragment atomic charges lie within 1 S.D. of the mean for 68%, and within 2 S.D. for 91%, of the atoms whose charges were computed for whole molecules. The actual charges on any atom are strongly influenced by the adjacent connected atoms. There is a large spread of atomic residual charge within the fragments database.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00125947
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  • 7
    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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  • 8
    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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  • 9
    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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  • 10
    Electronic Resource
    Electronic Resource
    Automated site-directed drug design: Searches of the Cambridge Structural Database for bond lengths in molecular fragments to be used for automated structure assembly (1992)
    Springer
    Journal of computer aided molecular design 6 (1992), S. 397-406 
    Details
    ISSN: 1573-4951
    Keywords: Drug design ; Molecular fragments ; Bond lengths ; Cambridge Structural Database
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary In this paper a database of small frequently occurring molecular fragments is used for the determination of fragment bond lengths from the Cambridge Structural Database. A large number of bond types are described that have not been reported previously.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00125946
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